Most of those arrested were Saudi citizens, but they also include people from six other nationalities, Al Arabiya News Channel reported.
The Saudi authorities said 190 suspects arrested were behind the Al-Qadeeh suicide bombing that killed 21 people and the Al-Asha gun attack that killed eight Shi'ite worshipers.
The ministry also said it arrested 144 others for "supporting Isis cells" in Saudi Arabia.
There were a number of terrorist cells with one, which was made of five members, tasked with preparing suicide bombers while another five-member cell had the mission to manufacture explosive belts.
The ministry statement said: "The number arrested to date is 431, most of them citizens, in addition to participants from other nationalities… six successive suicide operations which targeted mosques in the Eastern province on every Friday timed with assassinations of security men were thwarted."
The arrests were made over several weeks, but have only been announced by Saudi authorities on Saturday, Al Jazeera reported.
The announcement of the arrests comes after a car bomb exploded at a checkpoint near the kingdom's highest security prison on Thursday, killing the driver and wounding two security officials, according to Reuters.
Isis has recently been targeting Shi'ite worshippers in Saudi Arabia in a bid to ferment sectarian conflict and expel Shi'ite Muslims from the country.
Isis portrays the followers of the minority Muslim faith as heretics and apostates, according to the Council on Foreign Relations.
The militant Islamist group has killed 25 people in two suicide bombings at Shi'ite mosques in the country's east in May.
Saudi authorities said that seven attacks on mosques located in the capital Riyadh and the Eastern Province were also foiled.
Saudi Arabia is part of a US-led coalition carrying out air strikes against Isis militants in Syria and Iraq.
The militant group attacked a crowded marketplace in Iraq's eastern Diyala province yesterday, killing 115 people, including women and children, in one of the deadliest single attacks in the country in the past decade.