Abba Moro dismissed the attack as "desperate" and "isolated".
"The security agencies of Nigeria have been able to push the Boko Haram sect from their major strongholds," he told the BBC's Focus on Africa programme.
Nigeria has declared an emergency in three states after thousands of deaths in militant attacks in recent years.
Boko Haram is fighting to establish an Islamic state in Nigeria's mainly Muslim north.
By Will RossBBC News, Lagos
If this was Boko Haram, it might appear baffling. Many churches have been bombed but why would a group that wants to impose Islamic law across Nigeria open fire on worshippers at a mosque?
In fact this would not be the first time Boko Haram has targeted a mosque  - Muslim clerics have also been killed because of their views.
The gunmen may have known that amongst the worshippers were members of the vigilante groups that have sprung up to help the army defend the population.
Three months ago the military campaign was launched. But the Islamist militants have not been defeated - over the past month more than 160 people have been killed in attacks on boarding schools, army and police bases as well as a Christian-dominated area of Kano City. Other attacks go unreported. So what is the way forward?
One Borno state official suggests the only solution is to deploy more vigilante groups.
The mosque attack happened during dawn prayers on Sunday, although news only emerged on Monday, as communications have been disrupted by the state of emergency.
It took place in the town of Konduga, 35km (22 miles) from the Borno state capital, Maiduguri, where Boko Haram was established in 2002, launching its first attack seven years later.
Twelve further civilians were killed at Ngom village, closer to Maiduguri, reports say.
Boko Haram has not commented on the mosque attack but news of it came as a video emerged of the group's leader, Abubakar Shekau, saying his followers had carried out recent attacks including some that targeted the police and the military.
He said this showed that the army's claims to have inflicted heavy losses on the group were "lies".
It is not clear why the mosque was targeted - one explanation is that members of a local vigilante group may have been praying there.
Several such groups have been set up since the emergency was declared in Borno and two neighbouring states in May.
Boko Haram frequently attacks churches but it has also occasionally targeted mosques and preachers disagree with their views.
The attackers wore military uniforms, officials say, which they may have taken during recent attacks on a barracks.
Following a lull immediately after the emergency was declared, there has been a recent spate of attacks, blamed on Boko Haram, which have left some 160 people dead.
But Mr Moro said these were the "desperate antics" of a group trying to show it was still relevant.
Thousands of extra soldiers have been sent to the region since the state of emergency was announced.
The military cut mobile phone networks when they imposed the state of emergency, saying they wanted to make it more difficult for the militants to organise attacks.
However, some local officials have said this prevents civilians from getting help.

Charles Henry Chester, 86, from Bedlington was killed when his Nissan Micra collided with a Vauxhall Astra near Hartford Bridge.
Katherine Scott, 93, from the Morpeth area, and a passenger in the Astra, also died.
Its driver remains in the Royal Victoria Infirmary with injuries which are not thought to be life threatening.
Police have renewed a appeal for witnesses to the incident at 12:05 BST.
Nigeria's interior minister has said the army is making progress in the war against Boko Haram militants, despite the killing of 44 people in a mosque.
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Northumbria Police has named two people who died in a crash in Northumberland on Wednesday.