The Bogota bombing killed a civilian and wounded 15 soldiers before Alvaro Uribe, the country's president was sworn in for a second term last month.
The probe is the latest scandal to hit the security forces as they step up their fight against Marxist guerrillas and the drug trade that finances their insurgency.
"A recent car bomb which injured several soldiers and killed a Colombian and which was attributed to illegal groups, and the discovery of explosives over the last two months, appear to be false," General Mario Montoya, the head of the Colombian army, said on Thursday.
"These cons could have been carried out by a group of unscrupulous people who include two army officers."
Officials gave no reason for the soldiers' possible involvement in organising the attacks.
But analysts say a string of recent military scandals came as the government pressured commanders to show positive results from Uribe's security policies.
Officials had blamed the bomb attack on the Revolutionary Armed Forces of Colombia, or FARC, the country's largest rebel group that has waged a four-decade war against the state.
Uribe, a US-trained lawyer whose father was killed by the FARC, was easily re-elected in May after his tough stance against the Marxist guerrillas helped reduce high rates of kidnappings and killings that once bloodied the Andean country.
But thousands are still killed or forced from their homes every year by the conflict and rebels control rural parts of the country despite being forced back from towns and highways.
Earlier this year, an army commander stepped down after a scandal involving the abuse of recruits by officers, including beatings and rape at a basic training camp.
Human rights groups often say the army has cooperated with illegal right-wing paramilitary militias in the massacre of civilians in its war against the rebels.
A UN rights report this year said Colombian forces had killed civilians and covered it up by dressing the bodies as rebels to count them as part of the security success.