The Defra budget has been cut by £500m since 2010 and must find £300m in savings by 2016.
Defra spent £2.5bn during 2012-13, Efra said in its annual report on the department.
Efra select committee chairwoman and Conservative MP Ann McIntosh said: "Ministers must clarify how further budget cuts of £300m over the coming two years will impact on the funding provided to these agencies and the ability of the department to respond to emergencies."
A Defra representative said: "Like all departments we have to make efficiency savings but we are confident that our ability to respond to emergencies remains as strong as ever.
Severe and sustained flooding has affected many parts of the UK in recent weeks after the windiest December in the UK since 1969 and the wettest since 1993.
The Efra Select Committee report also said the department faced a number of other high-profile emergencies during the past parliamentary year.
These included the outbreak of ash dieback in the wider environment and the horsemeat food contamination scandal. Issues Defra faces in 2014 include Common Agriculture Policy reforms, biodiversity offsetting and GM technology.
The MPs observed that the allocation of resources to tackle these problems would be at the expense of other areas of policy.