Boro will have to pay £1m to the midfielder's former club Portsmouth if he reaches 100 appearances he currently stands on 99.
Portsmouth claimed over the weekend that their administrators are prepared to take legal action if the milestone is reached and Boro fail to cough up the due amount.
But Middlesbrough's chief executive Keith Lamb said: I am surprised by the comments attributed to a Portsmouth spokesman.
All of our payments to Portsmouth relating to Gary's transfer are up to date and I can assure the club and their administrator that should further payments become due under the terms of the transfer then we will of course honour them.
O'Neil, who manager Gordon Strachan claimed had picked up a knock
against Crystal Palace on Saturday, would reach 100 if he played at Plymouth today; triggering the final clause demanding the last £1m payment of the £4m deal Pompey agreed in the summer of 2007.
Boro made an initial £2m down payment for the midfielder and they also paid the £1m due when he reached 75 games.
But, with the further sixfigure payment due soon, Portsmouth allege the North-East club are trying to change the terms of the deal amounting to £20,000 for each of the five remaining Championship fixtures.
The Portsmouth spokesman had said: We can confirm that Middlesbrough have been in touch and have attempted to re-negotiate the payment terms regarding the final £1m payment.
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.
It is a situation which has led to Boro seriously considering leaving out O'Neil for the rest of the campaign.
Blackburn are believed to be among a number of Premier League clubs interested in signing the player during the summer so it would seem ridiculous to pay £1m for someone who could be moved in the coming months.
O'Neil is also one yellow card provided it is picked up before the second Sunday in April away from picking up his tenth caution and a subsequent two-match ban.
And Strachan, who will have a tight transfer budget to work with, knows gambling £1m of his potential fund for new players on a player that could be sold makes little sense.
Source: Northern Echo
Source: Northern Echo