Stone-throwing Nouakchott University students protesting against Silvan Shalom's visit clashed with riot police on Tuesday.
Police responded with batons and fired tear-gas grenades to disperse the protesters.
The visiting Israeli minister was greeted by his Mauritanian counterpart, Mohammed Fall Ould Bellal at the airport, before heading to a scheduled meeting with President Maaouiya Sid'Ahmed Ould Taya.
Shalom's visit was expected to last only hours in Mauritania.
Nevertheless, many Mauritanians accuse Ould Taya of bowing to foreign interests in maintaining ties with Israel.
The West African nation is one of only three Arab League countries with full relations with Israel.
Those protesting Shalom's visit burned Israeli flags and called on the Mauritanian government to close the Israeli embassy and cut diplomatic relations with Israel, Aljazeera reported.
Mauritanian authorities tightened security measures in the capital Nouakchott shortly before Shalom's arrival, Aljazeera's reporter in Nouakchott, Abd Allah Walad Muhammad, said.
Security forces had sealed off the university compound to prevent students from heading towards administrative headquarters, sparking fierce clashes with protesters.
Silvan Shalom will hold talks with
the Mauritanian president
Political parties, operating under the umbrella of the opposition, have expressed their strong objection both to Shalom's visit and normalisation of diplomatic relations with Israel.
Mauritanian authorities have said the visit is taking place in the context of ongoing progress in the Middle East peace process, and with a view to backing the efforts to achieve a settlement.
The country's political opposition, however, has slammed what it calls the government's opportunism, saying the authorities are using the visit to score points with the West.
Shalom is expected to discuss with Mauritanian officials the peace process in the Middle East, terrorist threats, and Iran's nuclear programme.
The Israeli embassy in Nouakchott has played down the significance of the protests and the anti-Shalom slogans on the city's walls, saying these would not affect Shalom's programme in the Mauritanian capital.
Mauritania established diplomatic relations with Israel in 1999.