Barry Lovejoy, the union's head of colleges, said the top priority for Ms Kelly as she settles into her new job must be "to get to grips with the financial issues in FE".
He added: "We hope she will use her skills as an economist to deal with the looming financial crisis."
He said the pay deal for college staff is based on funding promised under Success For All, the strategy drawn up for the post-16 sector by Charles Clarke, her predecessor.
"Now we are told funding doesn't match up to expectations," he added. "As a result, less than 10 per cent of colleges implemented the pay deal this year. And all the signs are that we are heading towards a crisis next year."
Ms Kelly was appointed in last week's Cabinet reshuffle which followed the resignation of David Blunkett from the Home Office. He was replaced by Mr Clarke.
An Oxford economics graduate, Ms Kelly was previously Cabinet Office minister after spending three years at the Treasury.
The Association for College Management said it hoped she would use her Treasury connections to help the post-16 sector.
Nadine Cartner, the association's head of policy, said: "The fact that she is in with the Treasury and well thought of by Chancellor Gordon Brown is good for us. We look forward to having a productive relationship with her."
The Association of Colleges said "threats to limit access to learning for aspiring young people and working women should be top of the new Education Secretary's in-tray". John Brennan, AoC chief executive, said: "We hope she will look again at funding plans which threaten access to learning for millions of adults. Women will be hit especially hard, forming as they do six in 10 of our adult students."
Alan Tuckett, director of the National Institute of Adult Continuing Education, said: "There are reasons for us to be cheerful about Ruth Kelly as Education Secretary. She has first-hand experience of the range of issues that family learning programmes throw up.
"She has played an active role in stimulating financial literacy which is of concern to older people."