Four French travellers were shot dead and a fourth wounded after they were attacked on December 24 in Mauritania's southern Aleg region.
A special police commission is to be set up to investigate any links with al-Qaeda, a Mauritanian security official said.
Both murder suspects have previously been arrested in connection with the Salafist Group for Preaching and Combat (GSPC), which in January 2007 affiliated itself with al-Qaeda.
The three alleged accomplices, meanwhile, were arrested on Friday evening in Bissau as they attempted to "film French (police) officers", said Mendes.
Authorities in Guinea-Bissau have said they were working with French anti-terrorism police to track the suspects.
"Guinea-Bissau will pay for what it has done. If I had a gun I would have killed you all," one of the five men shouted in the local Creole language as he was put on an aircraft by security officials.
Police in several west African countries launched manhunts after the roadside killing.
European states including France, along with the US, have also been co-operating to fight the growing presence of Latin American drug cartels using Guinea-Bissau as a smuggling hub to Europe.
The killings raised fears that fighters linked to al-Qaeda, who have carried out attacks in Morocco and Algeria, may be trying to extend their operations southwards into Sub-Saharan West Africa.
The incident led to security concerns and the cancellation of the 2008 Lisbon-Dakar rally which had been due to take place in January.