The Angkola Protestant Church, in the hard-hit South Tapanuli district, was festooned on Wednesday with balloons and simple Christmas decorations.

Outside, the street leading to the building was buried under mounds of debris and foliage.

Many in the congregation are still sheltering at evacuation sites after the disaster wreaked havoc on the island four weeks ago.

Churchgoer Krismanto Nainggolan said this year's Christmas service was "different", even as he noted joy in the bittersweet moment.

"The feelings are mixed. Every word of the pastor's sermon made us want to cry," he told AFP after the Christmas mass.

"But the spirit of Christmas... gave us strength," he added.

Krismanto lost his house in the flooding, while many of his neighbours were killed.

According to the National Disaster Mitigation Agency, 1,129 people died, and more than 170 others are still missing.

While the annual monsoon season often brings heavy rain to Indonesia, this month's deluge was among the worst disasters to strike Sumatra since a magnitude-9.1 earthquake triggered a massive tsunami in 2004.

In South Tapanuli, churchgoer Mea Rosmawati Zebua said she had not expected to be able to celebrate Christmas this year.

"In past years, Christmas was a routine. Now, (we are) very grateful because God still gives us the breath of life," the 54-year-old told AFP.

While Christmas mass is typically held in the evening, the Angkola church moved its service to Wednesday afternoon ahead of rain forecast in the evening, pastor Yansen Roberto Ritonga said.

To prepare for the first service since the disaster, the church had to remove towering heaps of mud that had been washed inside.

Soldiers and police had helped clear the debris and driftwood.

On Wednesday afternoon, a man rang the church's bell before the pastor's entrance, marking the start of the mass.

Around 30 worshippers, each of them holding a lit candle, sung Christmas hymns.

Yansen said this year's Christmas served as a moment of "reflection" for the congregation.

Churchgoer Krismanto said that despite the widespread damage and the personal cost of the disaster, he chose to see it as a new beginning.

"Our hopes depend solely on God because we are now starting over... our lives are starting anew," he said.