It said one sticking point over the extension of Chapman's one-year contract was the money the Bombers spent on Cooney, which was more than the three-time premiership player earned in 2014.
But the Bombers claim talks are on track and believe a deal will be reached.
"It was disappointing to see the story in Sunday's paper as we have been comfortable with how negotiations have been progressing over the last few weeks," football operations manager Rob Kerr told the club's website.
"Adrian Dodoro in his role as list manager has been negotiating with Paul's agent Liam Pickering on a new agreement.
"Those negotiations were continuing last week and we believe are headed in a positive direction with what we considered a fair and reasonable approach.
"Based on those discussions we feel we are fairly close to reaching an agreement with Paul given the way in which those negotiations have been progressing."
The 33-year-old played 20 games this season in his first as a Bomber and finished ninth in the best and fairest.
The 2009 Norm Smith medallist was reported to have had a trigger clause in his 2014 contract that required him to play a number of games to earn another year, which he achieved.
He signed the one-year deal with the Bombers in October last year when Geelong decided not to offer him another contract after he managed just eight games in 2013.
Pies do it again, Bombers look for No.11: Your club's best winning run
A pair of the longest active losing streaks in the League go on the line in round 10
Inaccurate Bulldogs bite back with Giant upset
The Western Bulldogs have defeated Greater Western Sydney by 27 points
Cruel blow as electric Crow pings hammy late, Pies' injury toll mounts
Izak Rankine and the Crows will sweat on scans after the midfielder suffered a suspected hamstring injury as he stormed towards goal in the dying stages against the Magpies
Around the state leagues: Young Dog, Cat star, is gun Swan in trouble?
Check out all the best players from this weekend's VFL, SANFL and WAFL action