The border between the two countries, both of which host Russian military bases, is poorly demarcated.
The Secretary General of Russia-led Collective Security Treaty Organisation (CSTO), Stanislav Zas, called for an immediate ceasefire at the border, RIA news agency reported.
It said Zas has held phone talks with senior security officials from Kyrgyzstan and Tajikistan.
"The armed confrontation at the Tajik-Kyrgyz border should be immediately stopped," he was quoted as saying by the news agency.
He also said that the CSTO, of which both countries are members, stood ready to help resolve the conflict.
Kyrgyz authorities said Tajik citizens had blocked a road between the provincial centre Batken and the Kyrgyz village of Isfana.
Border guards on both sides managed to get the road unblocked, but then fighting broke out.
The provincial government said no casualties had been reported but the Tajik service of Russian news service Sputnik reported that six Tajiks have been wounded.
Tajikistan's border guard service had no immediate comment.
An official from the local administration of the Tajik border town of Isfara wrote on Facebook that it was the Kyrgyz side which blocked the road.
At least 49 people were killed in fighting between the two countries last April which escalated from a similar border clash.
with reporting from AP
