"His (Justice Nizamul Huq) resignation reached to the law ministry through the registrar of the tribunal. He cited 'personal reasons for his decision'," Law Secretary Abu Saleh Sheikh Mohammmad Zahirul Haque told reporters.
Haque said the letter would now be forwarded to Bangladesh President Zillur Rahman and if he accepts the resignation a process would be launched to appoint a new chairman to the tribunal.
The International Crimes Tribunal-1 chairman Justice Huq's decision came days after The Economist magazine allegedly hacked his private conversation with Ahmed Ziauddin, a Brussels-based Bangladeshi-born war crimes expert.
A Bangladeshi pro-opposition newspaper published verbatim the leaked conversation in two subsequent issues.
Bangladesh Law Minister Shafique Ahmed later also confirmed his resignation but said Huq would continue to be a judge of the high court, where he was serving ahead of his appointment as the chairman of the tribunal.
Lawyers belonging to main opposition Bangladesh Nationalist Party and their ally fundamentalist Jamaat-e-Islami, whose stalwarts are being tried for war crimes charges, earlier demanded his resignation after the Daily Amar Desh published the reported conversation.
On December 5, the tribunal issued a notice on The Economist for "interference" in trial process and "privacy" of the judge and asked for an explanation in three weeks.
The two high-powered courts or tribunals currently try 10 high-profile Bangladeshi suspects of "crimes against humanity" accused of masterminding or carrying atrocities siding with Pakistani troops during 1971 Liberation War.
The tribunal also ordered a simultaneous investigation by police and Bangladesh Telecommunication Regulatory Authority into the hacking of Huq's conversation with Ziauddin.