"The Head of State decided... That these laws should be sent back to parliament for reconsideration," presidential spokesman Edson Macuacua told AFP.
Guebuza, 71, had "taken into account the opinions that arose around these laws," Macuacua added.
Some of the proposed perks included first class air tickets for the president and his family when they go on holidays.
Other perks included life-long retirement benefits for lawmakers -- even those who have served only a single five-year term.
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Despite rapid economic growth on the back of huge natural resource finds, Mozambique remains one of the poorest countries in the world with the majority of people in the country living on less than a dollar a day.
While Guebuza's salary is not made public, civil society groups claim that the president takes home close to fifty times the minimum wage, fixed last month at around USD 100 a month.
The opposition party Renamo welcomed the decision to review the bill but said it was a ploy to win votes for the ruling Frelimo party in the run up to October polls.
"This was clearly an electioneering move by the president of Frelimo, which is certainly regrettable," Renamo lawmaker Arnaldo Chalaua told O Pais newspaper.
This is not the first time that a Mozambican president has vetoed a law granting officials fat benefits. In 1998, Guebuza's predecessor Joaquim Chissano overturned a raft of retirement benefits for lawmakers.