It was not immediately clear if the killing in the oil city of Port Harcourt was related to a five-month campaign by militants to cripple the oil industry in the world's eighth largest exporter.
Late on Wednesday, a militant group said it had no hand in the killing.
In an email response to Reuters, the Movement for the Emancipation of the Niger Delta (MEND) said it was not involved in the shooting.
A diplomat and an oil company source earlier also said they did not think the rebels were involved.
Samuel Agbetuyi, Police Commissioner of Rivers State, said on Wednesday: "The American was shot by a man on a motorcycle. The motorcycle pulled up beside him and shot him."
Houston-based Baker Hughes, which drills wells and performs other services for major oil companies, was not immediately available for comment.
An oil industry source said the executive was being chauffeur-driven to work in the morning through a violent area when the gunman shot him through the chest.
The assassin was apparently working in coordination with a car which impeded the American's escape.
He could have been targeted because of a work-related dispute or some personal problem, the source added.
Members of MEND, whose attacks cut Nigerian oil exports by a quarter, have bombed oil facilities, kidnapped several foreign oil workers and recently embarked on a car bombing campaign.
However, they treated American oil workers well during the kidnappings, and the Port Harcourt killing did not bear any similarity to previous MEND attacks.
"It looks like a targeted attack on that individual, but my guess is that it was a private matter"
A diplomat said: "It looks like a targeted attack on that individual, but my guess is that it was a private matter."
The oil industry source said Baker Hughes had decided to pull its staff out of Port Harcourt to Lagos as a precaution.
Port Harcourt is the largest city in the delta, and several oil multinationals have major offices there, including Royal Dutch Shell and Agip.
Even if the attack is not linked to MEND, it adds to a trend of rising violent crime in the region, which pumps all of the OPEC member nation's oil.
Much of the violence stems from deep-seated resentment by many inhabitants of the delta, where impoverished villages stand close to multi-billion-dollar oil facilities.
Many residents feel cheated out of the riches being pumped from their lands.
Neglect and rampant corruption have eroded trust in government, while communal rivalries and abuses by the military have fuelled the rise of well-armed community militias.