Myanmar's President Thein Sein has issued his strongest challenge yet to “political opportunists and religious extremists” behind the attacks on Muslim communities in central Myanmar last week, saying on Thursday that his government “would not hesitate to use force” to curb the spread of religious hatred.

“In general, I do not endorse the use of force to solve problems,” he said in a televised address on Thursday night. “However, I will not hesitate to use force as a last resort to protect the lives and safeguard the property of [the] general public.”

Mr Thein Sein was returning from a visit to Australia when the violence broke out in Meiktila after a dispute in a turquoise beads shop between a Buddhist couple and the Muslim proprietor. Some analysts have blamed the president’s absence for the initial failure by other government leaders to order the security forces to act.

Police were seen standing by as mobs killed nearly 50 people and destroyed hundreds of homes, shops and religious buildings in Meiktila, where Muslims account for nearly a third of the 100,000 population. More than 24,000 people – at least two-thirds of them Muslim – fled their homes over three days of violence. About 12,000 people are now taking shelter in camps set up in schools, stadiums and monasteries.

At least 35 people have been arrested following the violence, and Mr Thein Sein said all perpetrators would be “prosecuted to the fullest extent of the law”.

“We will take all necessary and effective action to stop their operations in accordance with our constitution and our existing laws. All perpetrators of violence will be prosecuted to the fullest extent of the law.”

A state of emergency remains in place around Meiktila while curfews and bans on public gatherings have been imposed in at least nine other townships.

Mr Thein Sein’s speech was aimed not only at a general domestic audience but also at sending a powerful message to extremist Buddhist groups, including the 969 group led by the activist monk Wirathu, say analysts.

The speech also underlined the fragile nature of the government’s reform programme, which is aimed as much at reconciliatoon between opposing groups – ethnic, religious and political – as it is at economic development and promoting new freedoms.

Despite his assurances, the tension has spread to Yangon and other main towns and cities. Around the usually vibrant market area downtown, Muslim shopkeepers and money-changers have been closing early and some were seen this week reinforcing their shopfronts.

The president’s remarks followed an unusually pointed speech on Wednesday by Min Aung Hlaing, chief of Myanmar’s armed forces, emphasising the military’s intention to remain involved in national politics and to stem racial and religious conflict. “While the country is moving towards modern democracy, our military plays a leading role in national politics,” he told troops and dignitaries at a ceremony in Naypyidaw to mark Armed Forces Day.

The speech marked a shift from the military’s recent campaign against ethnic rebels in northern Kachin state  China beads, where ground and air assaults prompted thousands to flee their homes and led to international condemnation and accusations of human rights abuses.

In the audience was opposition leader Aung San Suu Kyi, who has been taken to task by some critics for making only brief comments on the religious violence. In her only public remarks so far, she said the violence showed the need to strengthen the rule of law and improve local policing.

In an unrelated but timely move, however, EU security experts are in Yangon this week to discuss a proposal to assist Myanmar with training on crowd control methods. The mission was prompted by the excessive tactics used by police to quell protests over a Chinese-Myanmar joint venture copper mine project in Monywa, in Sagaing state.

Ms Suu Kyi led an investigation into the incident, which dismayed some of her supporters with its conclusion that the project should proceed, although the commission stressed that locals – most of whom were against the mine – should receive more compensation for their land and for damages.