The deteriorating security situation Burundi and reports that Rwandan rebels are infiltrating the country are of ‘great concern’ to the Government of Rwanda, Foreigner minister Louise Mushikiwabo said in a statement on Monday night.

She called on the Burundian government to do everything in its powers to end the increasing unrest and violence targeting unarmed civilians.

“Rwanda urges the Government of Burundi to take immediate necessary steps to ensure the protection of its population, end the worsening humanitarian situation and restore peace. Rwanda has been particularly affected by the situation in Burundi,” Ms Mushikiwabo said.

It is the first time Rwanda has directly spoken out on the situation in Burundi since protests broke out three weeks ago, after incumbent President Pierre Nkurunziza was endorsed to seek another term in office.

Three people were shot dead on Monday by police as protests resumed after a weekend break, bringing the total of those killed to 12, according to Red Cross officials in the country.

President Paul Kagame has been mum about the situation in Rwanda’s neighbour to the south, despite meeting President Nkurunziza last month.

Rwandan President Paul Kagame (left) receives Burundian President Nkurunziza on April 13, 2015. Kagame has tactfully avoided commenting on the political situation in Burundi. PHOTO | FILE

By Monday, the number of Burundian refugees crossing into Rwanda reached 24,635, with 24,511 being sheltered in camps, according to the latest figures from the Ministry of Disaster Management and Refugee Affairs (Midmar).

Ms Mushikiwabo said that Rwanda takes seriously reports that members of Democratic Forces for the Liberation of Rwanda (FDLR) are crossing into Burundi.

“We take seriously the reports of links to FDLR, the hundreds of refugees crossing into Rwanda daily and, above all, the imperative of protection of civilians. We appeal to leaders of Burundi to do everything in their power to bring the country back to a peaceful situation. We will continue to work with the region and the international community to support peace,” she said.

The head of Police in Burundi denied reports that FDLR members and Interahamwe -- Hutu militia groups accused of carrying out killings in the 1994 Genocide against the Tutsi in Rwanda -- had crossed into Burundi to give support to the Imbonerakure, a local vigilante group linked to President Nkurunziza’s party.

READ: No FDLR militia here, says Bujumbura as Kagame mum on protests

The group, which has been allegedly trained and armed secretly, is threatening Burundians to vote Mr Nkurunziza or face death.

“It is not true, there are no Interahamwe or FDLR in Bujumbura, let alone in Burundi. These are rumours being spread to scare people,” the head of Burundian Police Ndereya Ndayambaje said last week.

Among its neighbours, Rwanda continues to watch the security situation in Burundi with concern, given that insecurity and political instability in the country could have a spillover effect on Rwanda.

“While we respect Burundi’s sovereignty in addressing internal matters, Rwanda considers the safety of innocent population as a regional and international responsibility,” Minister Mushikiwabo added.

Burundi’s elite flee

Hundreds of Burundi’s elite and working class are fleeing the country, with reports indicating that government employees, civil society and NGOs workers and members of the business community have also started fleeing the country.

Rwandan border authorities are recording a huge influx of Burundian registered vehicles while buses plying the Bujumbura-Kigali route are fully booked. Hotels and accommodation facilities are cashing in as the situation deteriorates further in Burundi.

“There is a group of Burundian elites particularly from the capital Bujumbura, who don’t go the camps like the ones fleeing from the villages in the northern provinces of Kirundo and Ngozi,” an immigration official who works on Kanyaru border post told The EastAfrican.

Majority of them have friends or relatives in Rwanda who help them arrange accommodation. The number of Burundian registered vehicles has increased in the capital Kigali.

Protesters have vowed to remain on the streets until President Nkurunziza rescinds his decision to contest in the June 26 polls.

Mr Nkurunziza, who has been in power since 2005, is facing stiff resistance from protesters calling for the protection of the 2003 Arusha Peace Accord which ended years of ethnic violence.

Former Burundi presidents Pierre Buyoya, Domicien Ndayizeye and Slyvestre Ntibantunganya have all spoken out againt Nkurunziza’s plans to seek another term.