General Hector Fabio Velasco said air raids in the region of Ituango have been conducted continuously since August and targeted two camps of the Revolutionary Armed Forces of Colombia (FARC) rebels.
"We know we have hit them very hard, they have a high number of deaths. Intelligence reports indicate there were 200 killed," he said.
There have been no independent confirmation of the army claims.
The army has launched massive offensives against the rebels and also right-wing paramilitaries since President Alvaro Uribe came to power in August, pledging to end the violence that has claimed about 200,000 lives since 1964.
Massive raids
General Velasco said no troops have been sent to the forested and heavily mined region, about 325 kilometres (200 miles) from the capital Bogota.
An Air Force spokesman said the death toll was based on technology aboard the aircraft and also reports from civilians in the area.
Earlier this month, General Velasco said that about 100 rebels had been killed during air raids of a rebel stronghold in southern Colombia.
Again, there has been no independent confirmation of the army claim.
US support
Meanwhile, a senior US military commander restated Washington's commitment to helping Colombia fight terrorism as he presented a Hercules transport plane to the Colombian Air Force.
"This is another symbol of the co-operation between the United States and Colombia," Army General James Hill said during the ceremony in Bogota.
"This is another sign that we fight together against the evil of terrorism."
The US provided more than $1billion in military aid to Colombia to target its huge coca crop, which winds up on US streets as cocaine.
Washington has also pledged its support for Mr Uribe's plan to beef up military campaign against the array of leftist insurgents and right-wing paramilitaries, whom the US accuses in drug trade.
Correspondents say this in effect means that there are no longer shackles limiting the use of hundreds of millions of dollars in the US military aid to narrowly defined counter-narcotic operations.
President Uribe is scheduled to meet the US President, George W Bush, in Washington, where he is expected to ask for more military aid.