Unless action is taken, either foreign officers could be recruited to fill the gaps or maritime jobs and businesses will move overseas, the House of Commons transport committee said.
The MPs also said the Maritime and Coastguard Agency (MCA) was taking on significant new responsibilities while its budget was being squeezed and was carrying "a sizeable number of vacancies in key posts".
Calling for a review of the MCA, the report said there was a risk that the agency "will increasingly struggle to discharge its regulatory responsibilities".
The committee also said it was "concerned that senior maritime professionals have suggested that budget cuts are undermining the work of the Marine Accident Investigation Branch (MAIB)".
The report went on: "We look to the MAIB's chief inspector to inform us if budgetary constraints prevent him from adequately discharging his duties."
The committee said in 2011 it had been predicted that within a decade, the UK would have 5000 fewer deck and engineering officers than the sector would require. The report said: "We recommend that the Government make an explicit commitment to address fully the predicted shortfall in trained seafarers by 2021."