Leaders of the ruling CPI(M) had accused the BJP of supporting the Indigenous Peoples Front of Tripura's (IPFT) statehood demand while campaigning.
Assam BJP leader and chairman of North East Democratic Alliance (NEDA), Himanta Biswa Sarma said his party believes in a united and vibrant Tripura, and it would never support separation of the state.
The BJP's alliance with the IPFT was "limited to ensuring socio-economic, linguistic, cultural issues of indigenous communities, he said.
"We believe in united Tripura. Our joint statement does not have anything to do with statehood demand," Mr Sarma said.
The joint statement, which was made available to the media today, stated that the ongoing initiative of the Ministry of Home Affairs to constitute an inter-ministerial high-level committee for in-depth studies of socio-economic, educational, cultural and linguistic status of indigenous population of the state would be completed at the earliest.
The panel was formed after IPFT leaders met Prime Minister Narendra Modi and Union Home Minister Rajnath Singh in New Delhi in January.
"Real proletariats of Tripura are indigenous people who were never on the developmental radar of the state," the joint statement said.
On the saffron party's prospects for the February 18 state election, Mr Sarma said that he has no doubt of victory against the Left Front in Tripura in the upcoming polls.
The BJP leader said "victory" over the Left Front in Tripura would be significant from the ideological point of view and the BJP wants to take the message from here to Kerala, where the CPI(M) is a major constituent of the ruling LDF alliance.
"Tripura will be the launching pad of achieving CPI(M)- mukt Bharat. After we win in Tripura, we will do the same in Kerala," he claimed.
IPFT president N C Debbarma had recently said that his party would continue to campaign on statehood demand despite forging an alliance with the BJP.
Asked about the issue, Mr Sarma said, "Different political parties might have their own agenda, but we are not aware of it. But BJP-IPFT alliance will work for the development of indigenous communities and the common minimum programme is the basis of the alliance, which is most important."
Under the terms of the alliance, the BJP filed nominations in 51 seats out of total 60 and IPFT fielded candidates in nine constituencies reserve for tribals.