The move pre-empted a censure motion, brought by 39 government deputies, most of them from the National Pact for Democracy and Development (PNDD), which heads the ruling coalition.
The deputies accuse the government of failing to deliver the required economic and social policy programme.
They have also questioned the share of government posts given to opposition Islamic and centre-left parties, as well as officials from the country's former administration, which was ousted by the military in 2005.
El Waghef described the dissensions within the PNDD as "very serious".
President Abdallahi instated El Waghef as his prime minister in May, trying to bolster his political power base as Mauritania faced threats from al-Qaeda attacks and rising food prices.
The censure motion had presented Abdallahi with his first major political crisis since he won elections last year, marking the return of civilian rule to the West Saharan state.