Fresh tensions between government and rebels in the two countries worst hit by the tsunami disaster threaten to undermine aid efforts.
US Secretary of State Colin Powell met survivors in southern Sri Lanka
In Sri Lanka, the Tamil Tigers have warned of serious consequences if government soldiers are not withdrawn from welfare camps.
They also continue to complain that little aid has been sent to rebel areas, despite government denials.
In Indonesia, the government and rebels have accused each other of attacks.
The authorities say that separatist fighters in Aceh province are exploiting the tsunami disaster and have provoked skirmishes with Indonesian soldiers.
The Free Aceh Movement, or GAM, has made similar accusations about government troops.
More than 140,000 people across the Indian Ocean region died in the tsunami disaster, while millions more are homeless.
US Secretary of State Colin Powell, who visited Sri Lanka's badly-hit southern town of Galle on Friday, has expressed hope that the "spirit of co-operation" in the aftermath of the tsunami would create new opportunities to resolve the long-running conflict between the government and the Tamil Tigers.
But the BBC's Frances Harrison says the disaster now looks likely to exacerbate ethnic grievances in Sri Lanka rather than help overcome them.
One rebel official warned there would be trouble if troops were permanently stationed in welfare camps.
The UN refugee agency, the UNHCR, has stepped into the row. Sri Lanka co-ordinator Neill Wright said: "The military is a wrong tool to manage these camps."
The tsunami swamped Sri Lanka's southern and eastern coastlines when it struck on 26 December.
Mr Powell toured southern areas by helicopter, making a stop in Galle, where US marines are to be based for relief operations.
After talks in Colombo with President Chandrika Kumaratunga, he said he would report on the tsunami aftermath to President George W Bush on Monday.
UN Secretary of State Kofi Annan arrived in Sri Lanka on Friday evening.
He will meet government leaders over the weekend. The Tamil Tigers say he has also accepted an invitation for talks in the north-east of the country with rebel leader Vellupillai Prabakharan.
In Indonesia, the country worst-hit by the tsunami, hopes are also fading that the disaster may pave the way for a solution to the long-running separatist conflict in Aceh province.
A ceasefire declared in the aftermath of the disaster has been strained by allegations of violence from both sides.
Mr Annan say the devastation in Indonesia is the worst he has seen
Indonesian soldiers say their relief work is being made difficult by sporadic clashes with separatists in Aceh.
In turn, the rebels have accused the military of using the disaster as a pretext for a renewed offensive, and have reported a number of casualties.
Neither allegation can be independently verified.
The US has warned Indonesia that military equipment provided to deal with the disaster should not be diverted for use in the fight against rebels.
It is now feared that more than 100,000 people have died from the disaster in Indonesia.
Touring the area by helicopter on Friday, Mr Annan said the devastation there was the worst he had seen.
"I have never seen such utter destruction mile after mile," he said. "You wonder where are the people? What has happened to them?"