The Football Association (FA) said Sampson's contract had been terminated with immediate effect, though the decision was not due to allegations that he made discriminatory remarks to one of his England players.
The 34-year-old Sampson, whose side beat Russia 6-0 in a World Cup qualifier on Tuesday, has been accused of discrimination by Chelsea striker Eniola Aluko.
Sampson, who took charge of the England team in 2013 after working with Bristol Academy, strongly denies the allegations and has been cleared of wrongdoing by two investigations -- one internal and the other an independent review.
The FA said it stood by the findings of the independent investigation, but another situation had emerged.
"In 2014, safeguarding allegations were made against him about his time with Bristol Academy," the FA said in a statement, without elaborating.
"The safeguarding assessment was that he did not pose a risk working in the game.
"However, the full report of that investigation was only brought to the attention of the current FA leadership last week and it is our judgement that it revealed clear evidence of inappropriate and unacceptable behaviour by a coach.
"It is on this basis that we have acted quickly to agree a termination of Sampson's contract."
Sampson replaced Hope Powell as England women's second permanent manager and led the country to third place at the 2015 World Cup in Canada.
England also reached the semi-finals of the European championships this year, losing to hosts and eventual winners the Netherlands.
"I have to say it is the most awkward and complicated issue I have ever dealt with," FA chief executive Martin Glenn told reporters at a hastily-convened news conference at Wembley Stadium.
He said no laws had been broken. But Sampson had "overstepped the professional boundaries between player and coach."
British sports minister Tracey Crouch said the situation was a mess and raised serious questions about whether the FA's historic processes around the recruitment of coaches were appropriate.
"The FA are right to have taken action but reassurance is needed to make sure this does not happen again at any level of coaching," she added.
(Reporting by Alan Baldwin; Editing by Ken Ferris and John Stonestreet)
