Peru produces more cocaine than any other country and anti-narcotics agents say most of it is smuggled to the US.
The bill was passed unanimously 89-0 and is expected to be signed into law by President Ollanta Humala.
However, officials say the US has expressed its opposition to restoring so-called aerial interdiction.
Peru halted the tactic in 2001 after an American missionary and her infant daughter were killed in an attack on a plane wrongly identified as carrying drugs.
The plane was brought down by the Peruvian Air Force but it was a joint operation with the CIA.
The US, which sponsors anti-drugs programmes across South America, has opposed attacks on suspected drug planes since then.
Other countries in the region - including Colombia, Brazil, Venezuela and Bolivia - already permit such planes to be shot down, albeit with strict guidelines.
Officials in Peru say about half of the cocaine crossing its border is being taken via small planes to Bolivia.
Peruvian congressman Carlos Tubino, who wrote the legislation, said the government could no longer allow traffickers to defy its laws.
Mr Tubino said there were about 600 drug flights a year in Peru, adding: "Just today there were two flights!"
President Humala vowed to make combating drug trafficking a priority when he took office in 2011.
His government has eradicated a record amount of coca crops with US assistance but has been criticised for seizing a relatively small amount of cocaine and leaving the air link to Bolivia undisturbed.
The Peruvian Congress has approved legislation that allows the country's air force to shoot down small planes suspected of carrying illegal drugs.