Kyrgyz interior ministry said casualties on its side had risen to more than 160, with 34 deaths – 31 of whom were civilians.
Kyrgyzstan has said a ceasefire with Tajikistan was holding on Sunday, as it accused citizens from its Central Asian neighbour of crimes during the pair’s worst clashes at their contested border in decades.
The Kyrgyz interior ministry said casualties on its side had risen to more than 160, with 34 deaths – 31 of whom were civilians.
The ministry also said it had opened 11 criminal cases against citizens of Tajikistan in connection with the violence, including investigations into murder and illegal border crossings.
Clashes between communities over land and water along the long-contested border are regular occurrences, with border guards often getting involved.
But the violence that erupted on Thursday was by far the most serious during the ex-Soviet pair’s 30 years of independence.
Tajikistan, a closed authoritarian state, is understood to have also suffered casualties and damages but has made far fewer statements on the conflict.
By Thursday evening a ceasefire deal had been drawn up, but Kyrgyzstan acknowledged that both sides had continued shooting on Friday and Saturday before the national security chiefs met to reinforce the ceasefire on Saturday afternoon.
Since then “no incidents of shooting have been registered”, a spokesman for Kyrgyzstan’s national security committee told AFP news agency by telephone at 11:00 GMT, describing the border as “quiet, peaceful, calm”.
The two national security chiefs also agreed on a border protocol early on Sunday, Kyrgyzstan’s main government website reported, offering few details on the agreement.
There was no immediate indication that progress had been made delimiting disputed sections which account for more than a third of the 971km (604 miles) border between the countries.
Al Jazeera’s Charles Stratford, reporting from Osh in Kyrgyzstan, said citing reports the situation in the area is “relatively stable”.
“We are hearing reports that the Tajik military has withdrawn back across the border, [and] we know that there has been a large mobilisation of the Kyrgyz army to that area,” he said.
According to local authorities along those borders about “58,000 people were evacuated from the area, 52,000 of whom they are reporting as being women and children”, Stratford added.
Kyrgyzstan on Sunday also accused Tajikistan of mistreating 10 citizens it said were taken hostage during the conflict before being released on Saturday evening.
The people, including the head of one of the border villages, were left bruised after being “beaten with sticks” during their abduction, Kyrgyzstan’s Health Minister Alymkadyr Beishenaliyev said.
“They showed us their bruises. We put nine of them [in hospital], one went to find his family,” the minister said.
Russia, which maintains military bases in the country, and neighbouring Uzbekistan said they were prepared to mediate in the conflict.
The clashes followed tensions between Kyrgyz and Tajiks over a key piece of river infrastructure on Wednesday.