Dr Jenny Harries said measures to bolster the NHS workforce by helping retired doctors return to work and social distancing measures had helped to an extent in reducing stress on staff.
But she warned that the mental impact of working through the coronavirus crisis would not be felt by healthcare workers until after the worst of the pandemic.
The deputy CMO told MPs on the House of Commons health select committee: 'I absolutely understand that it’s a very traumatic time and I think sometimes medics themselves are quite surprised at how much it has affected them.'
She added: 'I know that NHS England recognises that there is a considerable way [to go] after this. Often you get on with your job until it stops, and it’s the impact afterwards which is quite significant. I am aware that there is recognition, both of the impact now but also of the likely longer-term consideration that needs to be given in terms of support to staff.’
Dr Harries said that the estimated 20,000 nurses and 10,000 other healthcare staff who had returned to support the NHS workforce during the pandemic had meant that 'hopefully some of the really difficult stress will have been relieved' - although she acknowledged it could not be removed.
The warning comes as a BMA survey found that over a quarter of GPs were suffering from worse mental health during the pandemic, while a similar proportion said they were unable to access support.
More than two fifths of doctors said they were suffering from burnout, depression or anxiety during the pandemic, according to a BMA poll conducted last month.
Earlier this month NHS England launched a new mental health hotline offering support and advice through the COVID-19 outbreak. This allows doctors to speak with thousands of trained volunteers, who can give psychological support.
Government advisors, meanwhile, have said that waiting times for coronavirus test results is ‘coming down’ although 24-hour turnaround is yet to be achieved.
Dr Harries told MPs: ‘I think the time period for the test returns coming back is decreasing all the time.
‘I can’t give you a single figure because it will vary by the type of test and the way the test is being delivered and returned, but I am aware that [they] are coming down all the time and that reflects the capacity.’
The BMA has previously called on the government to ‘dramatically improve’ access to COVID-19 testing for frontline healthcare workers.