Managers at the Department for the Environment, Food and Rural Affairs (Defra) are facing suspicion they are discriminating against disabled staff.
MPs on the Commons' environment committee raised concerns about the issue in their 2012/13 annual report on the department's progress.
It noted the proportion of disabled staff receiving high performance marks, which put them in line for bonuses, was 19% - significantly lower than for the 27% seen for other staff.
Meanwhile 16% of disabled staff received the lowest performance mark, compared to just six per cent of non-disabled staff.
"We do not have evidence on the basis of one year's figures to determine any clear bias
against disabled staff, but the department must monitor this area to ensure that none
exists," MPs warned.
Defra has already introduced 'unconscious bias training' for its managers in a bid to combat the problem.
The committee's report has attracted headlines for its concerns about the harshness of the cuts faced by Defra, which has been under strain dealing with the consequences of ash dieback disease, horsemeat contamination and flooding.
It raised eyebrows that one-quarter of senior staff - the maximum permitted proportion - received bonuses of up to £12,000 last year.
That compares to 38% of non-senior staff receiving bonuses of up to £600, leading MPs to suggest a more equitable sharing of the bonus pool.
"Given the savings that the department must make over the next few years, we recommend that it review its practice on bonuses and consider whether, within government guidelines, increasing performance-related bonuses for those at the lower end of salary scales, with a consequent reduction for its higher-paid senior staff, might help to improve staff morale," the report stated.