Under new regulations enforced by European football's governing body from next season, no club should make an aggregate loss of more than 45million euros (about £39million) over the three seasons from 2011-12, or it will face being excluded from European competition.
He told the Guardian: "Clearly our intention is to comply."
Earlier this month City announced losses of £121million for the 12 months up to May 31, 2010, up from £92.5million for the previous year.
But Cook stressed the club do not plan to fall foul of the new rules, so will not head into the next transfer windows with the same "intensity".
Cook added: "Our two-year plan was to take a budget and build a competency to compete at the highest level, not forgetting the need for succession planning in every position.
"We are pleased with how that worked, and will not be signing players to the same level of intensity in the next transfer windows. Financial fair play is on our conscience. We talk about it at every board meeting, and it's part of our long-term plan."
Cook also hit back at critics of the club's recruitment policy after a summer spending spree of over £100million to bring in the likes of David Silva, James Milner, Mario Balotelli, Yaya Toure and Jerome Boateng.
He said: "Critics only have their own perspective. They're not at the football club. They haven't been part of the planning or the long-term financial strategies.
"People think we choose players from the fantasy football league but there was a clear plan for who Roberto wanted to sign."
Source: PA
Source: PA