It does not say how many people were killed in the clashes on the Tajik border, while Kyrgyzstan killed 336 people.
Tajikistan said on Monday that several people had been killed in border clashes with Kyrgyzstan last week in the first round of Tajik casualties.
Fighting between the two Central Asian nations began last Thursday with dozens killed and thousands displaced, but the fighting broke out on Monday after a ceasefire was broken on the same day.
The Prosecutor General’s Office in Tajikistan, a closed authoritarian state that has remained largely silent since the conflict began, says it has launched criminal investigations against members of the Kyrgyz army and armed civilians over the violence.
It said about 200 Kyrgyz army personnel and civilians who started throwing stones increased the unrest, leading to an exchange of gunfire.
“Several people have been killed and dozens injured in the armed attacks, and a large number of homes, border installations, other sites and infrastructure have been destroyed,” the statement said.
Clashes between communities over land and water along the long-rival border occur regularly, with border guards often involved.
But the violence that erupted in the Batken region on Thursday was the deadliest in the former Soviet country’s 30 years of independence and raised fears of an escalation.
Kyrgyzstan on Monday announced the death of a four-year-old boy in the fighting, which left 336 people dead and 18 injured.
Russia, which maintains military bases in the country, and neighboring Uzbekistan said they were ready to mediate.