The club's owner is seeking refuge in Britain after he and his wife skipped a court hearing in Bangkok.
"City's future is not in jeopardy," Cook told the Manchester Evening News. "In the short term, it is business as usual. We don't rely on Dr Thaksin's money.
"When Mark Hughes makes a decision we go through the normal process, which can include banks, finance, or a whole bunch of different things just like any other club."
Cook admitted that the former Thai Prime Minister might look in the long term to get extra investment in through 'partnership' deals.
"He is willing to look at whatever it takes to make City a great football club," said Cook. "This is a guy who loves City."
Cook spent time with Thaksin in Beijing before he returned to England.
"I gave him an update on the club and we talked about new player acquisitions," said Cook.
"We also talked over dinner about why he had bought the club and his intentions.
"It was really clear he wants to be at this football club for the next 10 years.
"He wants to build a dynasty and he was disappointed that people think he wanted to get in and back out."