The officer was shot at his home on Thursday in an upmarket residential area of the capital, Kathmandu. He was the most senior army officer to have been killed since the rebellion was launched in 1996.
"Maoist rebels entered Colonel Kiran Bahadur Basnet's house and shot at him at close range. He received five bullets and died in hospital," the army officer, who did not wish to be identified, told Reuters.
Another army officer shot separately by suspected rebels was being treated at the army hospital, the official said, adding that security had been stepped up in Kathmandu and across the Himalayan country.
No group has claimed responsibility for the attacks.
The rebels have been fighting since 1996 to replace the constitutional monarchy with one-party communist rule.
Despite having ended the ceasefire with the government, they have said they are open to fresh talks and have called for better understanding and trust between the two sides.
Nevertheless, the army is on high alert amid fears of a fresh wave of violence in the Himalayan country.
"The country can now look forward to a renewed period of instability and violence"
The Kathmandu Post
"The country can now look forward to a renewed period of instability and violence," the Kathmandu Post, said in an editorial.
The United States also warned on Wednesday of a possible new wave of attacks by the rebels, following the collapse of the ceasefire.
The US embassy in Kathmandu said that Americans could also become targets in the Himalayan kingdom, a day after issuing a statement criticising the rebels for an attempt to assassinate former Prime Minister, Sher Bahadur Deuba.
"Widespread attacks by Maoist insurgents on GON (government of Nepal) security forces and resumption of bombings in Kathmandu and other regions of Nepal could follow this break in the cease-fire," said the warning.
"The random, unpredictable nature of Maoist attacks creates risks of Americans being in the wrong place at the wrong time during a violent incident."
The peace drive collapsed earlier on Wednesday when the Maoists abandoned a seven-month ceasefire and peace talks, after the government refused their key demand of an assembly to redraft the constitution.
But a press statement issued by the rebel leader of the western region, Diwakar, who has just one name, said the attack on Deuba's motorcade on Monday, from which the former leader escaped unhurt, was a mistake.
Nepal, one of the world's poorest countries, was plunged into turmoil in June, 2001, when King Birendra and almost his entire royal family were massacred by the then crown prince in a drug-and-drink fuelled shooting spree.
The Maoist revolt has wrecked Nepal's tourism and aid-dependent economy and damaged its infrastructure.
Mainstream political parties are demanding King Gyanendra, Birendra's brother, should appoint a popular government. Last year the king dismissed the elected prime minister and replaced him with a royalist, in a row over the timing of elections.
More than 7800 people have been killed since the Maoists declared their "people's war" in 1996, aimed at establishing a communist republic.