The Pilgrims have been allocated just 878 of the 7,500 spots available for Saturday's contest at the LNER Community Stadium, where the winners will secure promotion from the National League North.
Despite being allocated 15 per cent of the tickets for the eliminator victory at Kidderminster Harriers and Sunday's semi-final success at AFC Fylde, this will not be repeated at the weekend due to the National League having nothing written in the rules to guarantee this is also the case for the final.
The National League promotion final will avoid similar problems due to it being held at West Ham United's 60,000-capacity London Stadium, leading some supporters to suggest the step two finals weren't taken into consideration when the rules were drafted.
York have home advantage due to them finishing higher in the league table.
"The away club in the eliminator and semi-final is entitled to 15 per cent of the capacity, but that doesn't apply to the final," club secretary Craig Singleton told BBC Radio Lincolnshire.
"The biggest game of the lot sees the away fans get the smaller allocation, which is baffling really.
"We were initially hoping we would get around 1,300."
The LNER Community Stadium has a capacity of 8,500 but this has been cut by 1,000 due to crowd problems in the club's home eliminator win against Chorley.
Local authorities made the decision following a pitch invasion and the letting off of flares.
Tickets will go on sale for Boston season ticket holders from 10am this morning.
The club has around 500 season ticket holders.
Tickets can be purchased in person at the Jakemans Community Stadium or on the phone from 10am today until 8pm.
The remaining tickets will go on sale to non-season ticket holders from 10am on Thursday.
A United statement read: "The Pilgrims are regrettably unable to sell and distribute tickets online due to differences within the respective clubs' ticketing and turnstile systems."
Tickets cost £20 for adults, £15 for concessions and £7 for under-16s.
York City have already sold out their allocation, with many regular supporters showing their anger online after being unable to secure tickets, despite many queueing for over an hour at the stadium.
The host club have also announced they will cancel any tickets for the home end they believe to have been bought by Boston supporters.
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