A Salafist is one of the main suspects involved in the killing, Interior Minister Lotfi Ben Jeddou said.
Gunmen on a motorbike shot Mr Brahmi, who led the Movement of the People party, in his car on Thursday morning.
The governing Islamist Ennahda party has rejected accusations from relatives that it was complicit in the killing.
In February, the murder of prominent secular figure Chokri Belaid sparked mass protests and forced then-Prime Minister Hamadi Jebali to resign.
‘Surprise’
Mr Ben Jeddou addressed a news conference in the capital, Tunis, that was broadcast live on national television.
“This information surprised us, the weapon used, a 9mm semi-automatic weapon, was the same weapon used to assassinate the martyr Chokri Belaid, not the same type, the same weapon, the same item,” he said.
Initial investigations pointed to Boubaker Hakim, a Salafist radical already being sought on suspicion of smuggling weapons from Libya, as the main suspect, he said.
Another man, Lutfi al-Zayn, was also mentioned as a suspect in the killing – both members of a 14-man group. Six other people were also being sought in connection with the assassination, it was announced.
Mr Ben Jeddou said extremists had benefited from the freedoms that flourished following Tunisia’s revolution in 2011 in which long-term ruler Zine al-Abidine Ben Ali was overthrown.
But following Mr Belaid’s murder, the arrests of dozens of militants had foiled their attempts to set up bases, with possible al-Qaeda involvement, in the mountainous region along the border with Algeria, he said.
Most of the suspects in the assassination of Mr Belaid were members of the radical Islamist group Ansar al-Sharia, he said.
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Analysis
Sihem HassainiBBC Africa, Tunis
“Who will be next?” is a question that many people are asking following the assassination of Mohamed Brahmi on Thursday. They fear that a hit list has been drawn up, with Mr Brahmi and Chokri Belaid, who was shot dead in February, being the first targets.
Mr Brahmi’s assassination took place on Republic Day, making many people conclude that the message of the gunmen was clear – they want to prevent Tunisia from becoming a democracy.
The suspicion is that regional instability is spilling over into Tunisia, with Algerian fighters linked to al-Qaeda in the Islamic Maghreb (AQIM) involved in Mr Brahmi’s assassination. The main suspect is already being sought on suspicion of smuggling weapons from Libya.
Rival Libyan militias have been fighting along the Algerian border, and people are worried that Libyan weapons and militiamen are increasingly finding their way into Tunisia. But it is the possible involvement of AQIM that worries people the most.
The minister ended the news conference by urging Tunisians who were demonstrating about the assassination to “steer clear of violence and the storming of sovereign buildings”.
Tunisia is experiencing a nationwide strike after the biggest trade union, UGTT, called the shutdown to denounce general “terrorism, violence and murders”.
On Thursday police used tear gas to disperse protesters in several towns, after Mr Brahmi was shot dead outside his home in Tunis in front of his wife and daughter.
Demonstrators attacked Ennahda’s headquarters in Sidi Bouzid, Mr Brahmi’s hometown and the birthplace of the Arab Spring revolutions which have swept the Middle East.
The BBC’s Sihem Hassaini in Tunis says Mr Brahmi was not a secularist, he was a socialist and practising Muslim with a pan-Arab ideology and even though he was from the opposition he did not have a reputation of being very critical of the Islamists.
He was not as prominent as Mr Belaid or as critical of Ennahda, which came to power in elections following the January 2011 uprising.
There has been deep division in the country between Islamists and secular opponents since Ennahda came to power.
The party has faced growing popular unrest over a faltering economy and a rising radical Islamist movement.
Correspondents say many Tunisians, particularly the young, complain that their quest for secular democracy has been hijacked by intolerant Islamists, including the Muslim Brotherhood which forms part of the current government.