Villas-Boas is on a two-year contract which ends in May and has already said he will not renew it. Firing him would involve paying a considerable amount of compensation but he made clear he does not want any money from the nine-time French champions.
On deadline day, the club made their fourth signing of the winter transfer window with the arrival of Ntcham on loan with the option to buy.
"I don't want anything from the club or Frank (McCourt), I don't want their money, I simply want to leave". I had specifically said no to that player and he was never on our list of targets. I've taken my decision to offer my resignation to the board.
"I was not aware of it, I learned of the signing when I woke up and went on the number one website for Marseille news".
Marseille said Villas-Boas' comments targeting Pablo Longoria, the director in charge of football, were "unacceptable" and raised the possibility of sanctions against the Portuguese coach following a disciplinary procedure. "I do not agree with the sporting policy".
"It's not the first time a player the manager didn't want has arrived at a club, but it's not how I work".
The 24-year-old has been capped by France up to Under-21 level and will hope turning out in Ligue 1 will boost his global ambitions.
It comes just three days after Marseille's home match against Rennes was postponed following violent scenes at their training ground.