The Trades Union Congress has called on leaders to provide more support for businesses to “stem the tide of redundancies” when the scheme ends in October.
Figures from HM Revenue and Customs show around 90,300 claims to furlough jobs were made in Lincolnshire by the end of June.
That was 12,100 more than at the end of May, and means 27 per cent of eligible jobs had been furloughed.
Under the job retention scheme, launched by Chancellor Rishi Sunak in March, the Government pays 80 per cent of employees’ wages, up to a maximum of £2,500 per month per employee.
Jobs at firms which are unable to operate or have no work for their employees because of coronavirus are eligible for furlough.
Across the East Midlands, 30 per cent of eligible jobs were furloughed by the end of June, while the rate was 31 per cent across the UK.
The figures show 9.4 million employments across the UK had been placed on furlough by the end of June, at a cost to the Treasury of £26.5 billion.
The scheme will be scaled back in August, when firms start making contributions to the costs, and will close in October.
Mr Sunak recently announced that employers will receive a one-off bonus of £1,000 for each furloughed employee who is still employed by January 31 next year.
However, the TUC warned it “falls short” of what is needed to prevent job losses.
General secretary Frances O’Grady said: “Mass unemployment is the biggest threat facing the UK.
“Struggling businesses need more than a one-off job retention bonus to survive in the long run.
“The more people we have in decent work, the faster we can move out of recession.”
The Institute of Directors, representing business leaders in the UK, said broader measures are needed to help companies which have “fallen through the gaps” of support throughout the pandemic.
A report from the Office for Budget Responsibility, the UK’s spending watchdog, predicts that 1.3 million furloughed workers may lose their jobs once the scheme ends.
Furthermore, different figures show around 26,400 people in Lincolnshire had applied to the Self-Employment Income Support Scheme by the end of June.
From May 13, eligible self-employed workers could claim a grant worth 80 per cent of their average monthly profits for a three-month period, limited to £7,500.
Claims made by people in Lincolnshire amounted to £75.7 million, or £2,900 per person on average, with 72 per cent of those thought to be eligible in the area having asked for support.
Self-employed workers can claim a second and final grant in August, lowered to 70 per cent of profits and capped at £6,570.
The Association of Independent Professionals and the Self-Employed said there was a “noticeable absence” of support for the self-employed in Mr Sunak’s announcement.
Andy Chamberlain, IPSE’s director of policy, said: “While the Chancellor has announced a measured and sensible end to the employee furlough scheme in October, freelancers are left to face a cliff-edge in August.”
A tapered end to the SEISS would “address the imbalance” between employees and self-employed people, he added.
A Treasury spokesman said applications for the final grant will remain open until October 19, making it “among the most generous schemes in the world”.
“Many self-employed people will benefit from the jobs created through the Plan for Jobs,” he added.