Sidi Ould Cheikh Abdallahi, the president of Mauritania has been visiting policeman who are being treated in hospital after being injured during the gun battle.
Mauritanian police said that the dicovery of an operational bomb factory in the abandoned house indicated the presence of a "terrorist" cell in the capital.
Mohammed Abdallahi Ould Adda, from Mauritania's judicial police force, said: "We found an expllosive device they were preparing to detonate in case the house was assaulted by the security forces."
"We also found a laboratory poised to produce explosives, " added Adda.
However, the police withdrew an earlier claim that Sidi Ould Sidna, a fugitive with al-Qaeda links, wanted for the murder of four French tourists, was among those arrested on Monday, after the raids.
"He is still on the run," said a source from the Mauritanian police.
Security sources said a car with five or six people managed to get away during Monday night's clash, under the cover of fire from men inside the house.
Security officers said, they later found a wounded man in an abandoned car and one of their officers mistook him to be Sidna.
Sidna had earlier escaped from a courthouse last week, after an interrogation session.
The Mauritanian government has, meanwhile, announced that it would crack down heavily on extremists.
Aziz Ould Dahi, a government spokesman, said: "I want to affirm in the name of the republic and in the name of our government, our determination to fight terrorism in all its forms, and our willingness to continue to meet it with force."
Another source from the Mauritanian security force added, on conditions of anonymity, that these were the first raids where the government had used many small aircraft to hunt down the suspects.
"Planes were used for the first time on Tuesday to comb through dunes by the seashore and north of Noukachott, where the runaway terrorists can naturally take refuge," said the source.
Mauritania has seen little terrorism so far.
However, increasing security concerns led to the cancellation of the Lisbon-Dakar rally, which was due to pass through Mauritania in January this year.