ThThe General Medical Council said the scale of the action, planned at such short notice, could not be justified.
The first of four five-day walkouts is due to begin from 12 to 16 September, with the last being in mid-December.
Junior doctors are striking over a new contract which is being imposed.
The GMC has set out advice to doctors before next week's series of one-day strikes and voiced a stronger warning than previously about the possible impact of the strike action.
GMC chair Prof Terrence Stephenson, said doctors have a right to strike but they must consider whether it will cause significant harm to patients.
The GMC will investigate any case where a patient has come to significant harm because of actions by a doctor.
Prof Stephenson told the BBC's Today Programme: "The idea that you can take a third of the workforce out of a busy emergency service for five days and have no consequences seems to me unlikely.
"We are quite clear in our guidance that every single individual doctor most put their patients first. And we make it clear that they are personally accountable for their actions and must be able to justify what they did afterwards if allegations our made against them."
He urged every doctor in training to "pause and consider the implications for patients."
Meanwhile, Chris Hopson, of NHS Providers, said: "The GMC is right to be 'extremely concerned' about the impact the series of strikes by junior doctors will have on patients.
"We share the GMC's view that the scale of action planned at such short notice cannot be justified."
Consultants will cover junior doctors in providing emergency care, as they did during two days of walkouts in April.
Hospitals will see junior doctors stage walkouts from 08:00 to 17:00 from:
- Monday 12 September to Friday 16 September
- Wednesday 5 October to Tuesday 11 October (although the weekend will be covered)
- Monday 14 November to Friday 18 November
- Monday 5 December to Friday 9 December
PA
The warning from the GMC comes after senior doctors last week urged the government and junior doctors to restart negotiations to avoid the series of strikes.
While some medical colleges have said the planned strikes are disproportionate, others say they support the junior doctors' stance.
The row over their pay and conditions has escalated into the worst industrial relations dispute in the history of the NHS.
The BMA has said the government could stop the strikes by calling off the imposition of the contract, which is due to be rolled out from October.
A spokesman said: "Patient safety remains doctors' priority and, since the announcement last week of further action, the BMA has been liaising with NHS leaders so that plans can be put in place swiftly to minimise disruption for patients."
But Prime Minister Theresa May last week told doctors to stop "playing politics" in the dispute and urged the union to cancel the strikes.
The imposed contract
PA- Basic pay to rise between 10% and 11% on average
- Supplements paid for frequent weekend working - those working one in two will get 10% on top of basic salary
- Nights to attract an enhanced rate of 37% above normal time
- Replaces old system whereby weekend or night work can attract up to double time
- First doctors to go on new terms in October with much of the rest of the workforce to follow by next summer
- The British Medical Association says it is not fair on those who work the most weekends or part-timers
Junior doctors have already taken part in six strikes this year, including two all-out stoppages.
Industrial action was put on hold in May when the two sides got back round the table at conciliation service Acas.
That resulted in the agreement of a new contract, which BMA leaders encouraged members to accept.
But when it was put to the vote, 58% of medics rejected it, prompting the resignation of the BMA junior doctor leader Johann Malawana and causing ministers to announce once again that they would impose the new terms and conditions.
