Bangladesh is braced for violent protests following the hanging of an opposition politician convicted of war crimes committed during the brutal civil war that led to the south Asian nation's independence more than 40 years ago.

Abdul Quader Mollah, a senior official in the Islamist Jama'at Islami (JI) organisation, is the first defendant to be hanged by a controversial special tribunal set up by the Bangaldeshi government three years ago.

Security forces are preparing for violence on Friday and at the weekend. JI officials have called a nationwide strike for Sunday.

Mollah was found guilty by the International criminal tribunal in February of killing a student and a family of 11 and of aiding Pakistani troops in killing 369 other people during the independence war. He was sentenced to life in prison, but the supreme court changed that to a death sentence in September.

After a last-minute appeal by lawyers was rejected, the 65-year-old was hanged in a prison in Dhaka, the capital, just after 10pm (4pm GMT) on Thursday.

The tribunal has been criticised by human rights activists and legal experts as deeply flawed. It has held a series of trials of individuals accused of war crimes committed during 1971 war. Most of the defendants are opposition members, leading to charges that the process is politically motivated.

Senior officials from the ruling Awami League reject the accusation and say the trials are necessary "to exorcise the ghosts of Bangladesh".

"Is it up to the international gold standard? The standard of the Old Bailey? No. But does the tribunal match, indeed exceed, the standards of our usual courts here in Bangladesh? Yes it does," said one.

Hasan Jamil, the eldest son of Mollah, told the Guardian the execution of his father was "a political killing" orchestrated by the government to allow them to declare an emergency when the street violence that the hanging is likely to provoke occurs.

"After this injustice no people can stay home. They will organise big demonstration. The government may declare emergency," he said.

Shantanu Majumder, political analyst, termed the hanging a "big step forward towards the political development of Bangladesh".

The hanging comes at a fraught political time with the opposition, led by the Bangladesh Nationalist party, already committed to boycotting elections called for January. Jamaat Islami was effectively banned from participating in the poll earlier this year.

Bangladesh has been partly paralysed by a series of shutdowns and strikes called by the opposition in recent weeks. Hundreds may have been killed in street violence this year and many more injured.

On Thursday JI activists clashed with police, torched or smashed vehicles and exploded homemade bombs around the country, TV stations reported.

In eastern Bangladesh, security officials opened fire to disperse opposition activists, leaving at least three people dead and 15 others wounded, Dhaka's leading Bengali-language newspaper, Prothom Alo, reported.

More such incidents are expected in the run up to January's poll.

Much of the political instability that troubles Bangladesh can be traced back to the 1971 war or its immediate aftermath. More than three million people died, some say, in one of the most violent and bitterly fought conflicts in the region in recent decades.

Forces from Pakistan sought out and shot thousands of intellectuals and political leaders in Dhaka in a bid to crush the movement for an independent Bangladesh. They were assisted by local collaborators, many linked to the JI organisation. Asif Munier, son of a university teacher who was killed in 1971 for supporting independence, said he was pleased with the court's decision to reject Quader Mollah's last-minute appeal.

"Yes, we are happy because justice has been served … It's not about any revenge," Munier said after the supreme court decision.