The seizure comes days before polling in the coup-prone West African country.
A spokesman for Muhammad Khuna Wald Hidala, a former military ruler of the Islamic republic, said one of the guns was a gift and that Hidala had borrowed the second to give to his bodyguard.
Police said they had seized guns and ammunition but did not specify from where.
Hidala, 63, is seen as President Muawiya Wald Sidi Ahmad Taya's strongest challenger in Friday's presidential election.
The election comes only five months after loyalist forces put down an attempted coup in two days of street fighting in the capital Nouakchott.
Hidala seized power in 1980 but four years later was ousted by Taya in a coup.
He has assembled a broad coalition of supporters ranging from reformist liberals to Islamists, the people Taya blamed for the coup attempt in June.
"We have a tradition of keeping weapons at home, either for hunting or target shooting," Hidala's spokesman Ely Wald Snaiba said.
He had earlier said that no weapons had been seized during the search, denouncing it as a provocation ahead of the poll.
Police said in a statement they had carried out searches in several places after some Hidala aides told them so-called extremists in his camp may have stashed weapons in houses and mosques.
Aisha Bint Jidanah is the first
woman contending the elections
They said some Hidala aides were concerned that the extremists might revolt if the election results were not in Haidalla's favour.
According to Aljazeera’s correspondent in Mauritania, a Muslim leader supporting Hidala, Shaikh Muhammad al-Hasan Wald al-Daddu, was detained briefly after weapons were found in his home.
Since independence from France in 1960, power has never changed hands through the ballot box in Mauritania.
Taya, described as pro-Western, has performed a stunning diplomatic about-turn over the past decade, shifting from supporting former Iraqi president Saddam Hussein to establishing full relations with Israel in 1999.
That has made him unpopular with Arabs in his country. Like Taya, Hidala hails from the "Bidan" Moorish community, which has formed the ruling elite since independence.
Besides him, four other opposition candidates are contesting the election.
For the first time, a female candidate, Aisha Bint Jidanah, 43, is vying for presidency. Another contender is Masaud Wald Bilkhair, the first descendant of slaves to run for president in Mauritania.