Nigerian President Muhammadu Buhari condemned the attacks, as did the US embassy in Abuja.
"The death toll is now 18 because three people died in the hospitals this morning while 41 others were injured and are receiving treatment in the hospitals," Sani Datti, spokesman for the National Emergency Management Agency, told AFP.
The blasts took place late yestersay near a police station in Kuje and at a bus stop in Nyanya, in an area previously targeted by Boko Haram militants.
The Inspector-General of Police, Solomon Arase, had ordered massive stop-and-search activities in the city and advised residents not to panic, the force said in a statement.
"Following the incidents the police high command ordered an immediate deployment of police explosives ordnance disposal units to the scenes to prevent further destructions," it said.
An AFP reporter saw four wounded patients at Kuje hospital with 18 more injured at other medical facilities. Kuje residents were shocked over the tragedy as a heavy military presence surrounded the bomb site.
Idris Abdulkareem said "a lady and a guy" who came on a motorcyle had set off the blast. He said the "guy" left the bike and said he would be back in a few minutes.
"The moment he left the bomb sparked (went) off," Abdulkareem told AFP.
Kuje, near Abuja's airport, is around 40 kilometres (24 miles) from the city centre and seat of government.
The Kuje prison has been reported to be holding dozens of Boko Haram prisoners captured by troops.
The bus station in Nyanya had previously been hit twice last year. The first attack,on April 14 left at least 75 dead and was claimed by the Islamists; the second on May 1 left at least 16 dead.
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