"Elements from abroad, supported by some obscure forces within the country, carried out these attacks. Some of them have been arrested," a junta officer said in the television message.
Minutes earlier the junta issued a scrolling message over state television claiming it remained in control of the state broadcaster building, the airport, and a major military base in Kati, just outside the capital Bamako.
Fighting erupted late on Monday with presidential guard units loyal to ousted President Amadou Toumani Toure deploying throughout the capital.
A Reuters witness near the broadcaster's main building said that gun and heavy weapons fire continued near the building into Tuesday morning. Another witness near the airport added gun fire was also continuing there.
A Reuters witness overnight saw a pro-junta military officer in the capital standing over two corpses in presidential guard uniforms, showing what he said were tribal tattoos proving they were from Burkina Faso.
Mutinous soldiers angered by the government's handling of a rebellion by Tuaregs in the vast desert north toppled President Amadou Toumani Toure on March 22, forcing him to flee the country for neighbouring Senegal.
The coup, which pre-empted a planned April election meant to replace Toure, has drawn broad international criticism as a major setback for regional democracy. The northern rebels took advantage of the chaos to seize several northern towns, effectively taking control of two-third of the nation.
Mali's ruling junta has named an interim government in a first step to restoring constitutional order since the coup, but it has balked at a plan by regional bloc ECOWAS to send more than 3,000 troops to help oversee a one-year transition.