The pair, who were working with Nigeria's National Commission for Museum and Monuments, were seized at about 8:55 am (0755 GMT) as they worked at an excavation site in southern Kaduna on Wednesday.
Federal police chief Ibrahim K. Idris said the men had been assigned security personnel for their own protection but that they did not go with them to the dig site into ancient Nok culture.
Surveillance helicopters and anti-kidnapping and counter-terrorism officers have been deployed in the hunt for the perpetrators, he added.
"The abductors came wielding guns and machetes and asked the two Germans to follow them into the bush," said a resident who asked not to be identified because of security fears.
"Surprisingly, they did not kidnap the two female German colleagues of the men. They fired shots into the air to scare off the villagers before abducting the Germans," he added.
The local and police chief Idris both said two locals were killed.
Safety on the road has come under intense scrutiny in recent weeks since the federal government announced the closure of Abuja's only airport for essential runway repairs.
All domestic flights will be diverted to Kaduna from March 8 for six weeks but international carriers have refused to re-route their services, reportedly because of fears about capacity.
In July last year, Sierra Leone's defence attache to Nigeria was kidnapped by armed men with AK-47 assault rifles in military fatigues at a fake check-point on the Abuja-Kaduna road.
Extra checkpoints could add several hours on to journeys following a renewal of long-standing violence between herdsmen and farmers in southern Kaduna since December last year.
Some estimates say the clashes between the Muslim, largely Hausa-speaking Fulani cattle drivers and mainly Christian farmers have left as many as 800 dead. But the official toll is about 200.
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