Portsmouth claim Middlesbrough are trying to renegotiate the final payment on the deal which took Gary O'Neil to the Riverside in 2007.
Boro have so far paid £3million for the midfielder and are due to stump up a further £1million when O'Neil plays his 100th game for the club.
The 26-year-old reached the 99 mark in Saturday's 1-1 draw at home to Crystal Palace and another outing would trigger a payment to troubled Portsmouth.
Pompey say Boro want to change the terms of the final payment, but the Premier League's bottom club have suggested their administrators will not agree to a renegotiation.
"We can confirm that Middlesbrough have been in touch and have attempted to renegotiate the payment terms regarding the final £1m payment due to the club," a Pompey spokesman told the Sunday Mirror.
"The administrators are absolutely furious.
"They have told Middlesbrough in no uncertain terms that they will take legal action if they fail to honour the contract in place."
O'Neil, who has a further two years to run on his contract, is a doubt for Boro's game at Plymouth Argyle on Monday after picking up a knock against Palace.