The BBC investigation comes in response to anger the levies businesses pay for events and marketing are only being deferred for six months - and not scrapped altogether, as is the case with business rates.
Concern about the deferral was raised locally by many businesses which have been forced to close during the Covid-19 pandemic. However, government legislation has meant the levies still have to be collected.
Tony Kelly, general manager of the Lookout, said: "I have been in the business for 30 years and this is the most serious situation we have seen - something we could never have planned for.
"For us to have to pay to attract people to come here when they shouldn't is a waste of money."
Coun Danny Brookes owns Indulgence cafe in High Street and runs kiosks on the foreshore. He told the BBC: "As you can see the streets are empty and without the summer trade Skegness will be in big trouble.
"The problem is, we need the money right now - we are earning nothing right now. So if they are going to charge us for the future, there's a lot of businesses that might not be here in the future."
He later told the Standard: "The Government has taken steps to help us in these tough times and yet the BID still wants its pound of flesh - this cannot be right.
"I supported the BID at the beginning because I thought it would be good for Skegness and the coast but this hasn't developed.
"BIDs all over the country are failing - businesses are not happy."
Payments vary from a few hundred pounds to thousands. "It may not seem a lot but £200 is a lot of breakfasts we have to sell," said Barry Robinson, who runs Lite Bites on Roman Bank.
Lincolnshire Coastal BID is now in its third year and a Facebook page - East Coast Against the LEVI (BID) - has been launched by, in the main, small businesses intent on the BID not being voted in for a second term because they do not feel they have benefited from any of the events or promotions their cash has paid for.
The businesses we spoke to said it was unfair to be expected to pay anything at all to the BID during the lockdown when nothing seemed to be happening.
They were also upset that two members of staff - a new manager, Nicola Mcgarry, and assistant Angie Robinson - had taken up their roles during lockdown to replace former manager Lisa Collins and Harriet Lawson, whose 'amicable' resignation was reported at the beginning of the year.
A statement by Nicola Mcgarry and BID chairman Coun Sid Dennis, said the organisation was 'determined to support levy payers' through the lockdown and return 'return stronger than ever'.
The statement said: "We appreciate that COVID-19 pandemic has had an enormous impact on all businesses within our BID area and nationally.
"We also understand that some businesses are in a position where they are reviewing every expense they currently have due to these difficult times.
"To the majority, however, Lincolnshire Coastal Destination Bid is a significant and positive channel to pool our resources and to focus on our key objectives. We are determined to support our levy payers through the means of the destination BID as much as we are able to and believe that once through these difficult times, all those whom have been affected will return stronger than ever.
"We should be mindful that the average business paying approximately £370 per annum is creating a pool of approximately half a million pounds per annum which is then reinvested into the coastal strip and the benefits of this is clearly realised through the work that has previously been completed since the BID was established in 2017 and will do so going forward.
"We must take a united front and understand that only by working together positively and with community spirit, we will then be in a strong position to promote the area and ultimately recover the footfall lost when businesses reopen.
"We are passionate advocates of our four values which are; Marketing and Promotion, Environmental Enhancements and Access Schemes, Events, Business Support and Networking."
They said some of the events cancelled due to COVID-19 restrictions are hoped to reschedule later on in the season,
"We will constantly monitor government advice and guidance. Preparations are currently being made for events, marketing and promotions and other projects for 2021
"As well as the many successful events that have been organised, we undertake various advertising and communication campaigns, helpful links and information to support our people through COVID-19, all via our website VisitLincscoast.co.uk, numerous social media streams, our destination guide, advertisements through contracts with bus/coach companies and HGV suppliers travelling nationwide.
"There has also been a radio campaign, promotional video, a banner along the seafront and in bus shelters - all to promote our beautiful coast and the services and activities within.
"Recently, we have partnered with other BIDs and organised support webinars to aid those in this difficult time. We will continue to support as much as possible where we can.
"We also have a team of Rangers who assist in keeping the BID catchment safe and clean as well as having a strong customer focus and working alongside our emergency services/CCTV organisations as well as our Business Watch scheme. We are also currently supporting a major new project to improve skills for business owners and their staff members.
"We have been able to negotiate a deferment of levy payments until September however to clarify, we as a Board are not legally empowered to NOT collect the said payments.
"Under Government regulations, a BID is required to operate within, it cannot raise or adjust the levy invoices themselves nor the levy rules, as described in the original BID Business Plan which must be strictly adhered to.
"However, should the Government relax the regulations due to the current COVID-19 situation, as we have previously stated, we will review the process in line with Government legislation and recommendations.
"We are advocates of the ‘Raise the Bar’ campaign and are strongly in support and lobbying the government to waiver the levy this financial year."
Regarding the recruitment process for the replacement of two staff members, they said the appointments were made prior to the lockdown and following the 'amicable' resignation of their predecessors. Additionally, two staff members known as ‘Rangers’ are currently under the Furlough scheme to be reviewed in the coming weeks.
"In addition, you will be aware that the Government on Friday announced £6.1 million funding boost to help high streets and town centres through the pandemic," they said.
"This funding is of course welcomed, but the scale per BID, flexibility of use and timing is still unclear. There are in excess of 200 BIDs in the UK. This will help but, in reality, the scale is unlikely to allow for significant change, rather to help with the short term sustainability, similar to the Visit Britain COVID-19 Support Grant we were recently successful in receiving."
A spokesman for East Lindsey District Council: "The council voted in favour of the BID, we are a contributing levy payer and we remain supportive of the work they do along the coast.
"They perform a very different role to the GLLEP’s Visitor Economy Board and work on a more local level to support businesses and work in partnership with them to promote the Lincolnshire Coast.
"Ultimately we can’t pre-empt the future of the LCDBID as this will be a matter for businesses to vote on, just as it was when the BID was established."