Mr Tomlinson told MPs on the education select committee that inspectors had warned him that schools were having to cancel "essential" geography and biology field trips to the countryside for GCSE and A-level students.
"Of course, the worry... is how that will impact on (pupils') overall grades. Clearly it would be a worry for the pupils," he said.
Mr Tomlinson also disclosed that two school inspections have been postponed in recent weeks because of the outbreak.
Liberal Democrat education spokesman Phil Willis this week called on Education Secretary David Blunkett to issue "urgent advice" that exam grades would not be affected by the crisis. The Joint Council for General Qualifications, the umbrella body for the three main exam boards, has issued advice that schools planning fieldtrips in rural areas should "make every effort to put in place alternative arrangements".
Where possible, schools should carry out the work locally. Any school experiencing problems with the foot-and-mouth outbreak should alert the exam board to the problem. The joint council indicated it would take pupil' difficulties into account in grade calculations. Mr Tomlinson had no figures on the number of pupils affected. Nor had the joint council.
Meanwhile, pressed by MPs on the current teacher shortage, Mr Tomlinson followed Education Secretary David Blunkett in refusing to describe the shortfall as a "crisis".
He said the Government needed to adopt a long-term strategy for tackling recruitment and retention, but added that the numbers entering the profession always followed the economic cycle, with recruitment particularly difficult during prosperous times.
The committee was told that inspectors plan to get tougher with schools at risk of failure, amid signs that heads and governors are not taking seriously the need for improvement.
Elizabeth Passmore, head of inspection, told the select committee that one in five schools judged by inspectors to have serious weaknesses was still underachieving on a return visit 6-18 months later.
Inspectors currently do not return to check on all schools with serious weaknesses.
Miss Passmore said: "We should consider whether, instead of visiting a sample and giving them a year, we need to visit rather more, and rather more rapidly."