Hillary Clinton said Sunday Saudi Arabia's recent execution of 47 people, including Shia Muslim cleric Nimr al-Nimr, raises "serious questions" that the US needs to ask the country's government.

Saudi Foreign Minister Abel al-Jubeir announced the bombshell decision late Sunday, giving Iranian diplomats in Saudi Arabia 48 hours to leave the country.

Ellie Geranmayeh, an Iran expert at the European Council on Foreign Relations, said the Saudi decision was likely to have repercussions in the region, particularly concerning the Syrian negotiations.

Saudi Arabia says it has broken diplomatic ties with Iran, after protestors stormed the Saudi embassy in Tehran over the weekend.

Nimr's brother said he was found guilty of seeking "foreign meddling" in the kingdom, "disobeying" its rulers and taking up arms against the security forces. Iran and Saudi Arabia also support opposing sides in Yemen, where Saudi Arabia has been launching airstrikes against the Iran-backed Houthi rebels since March.

Earlier on Saturday, Iran's Foreign Ministry summoned Saudi Arabian charge d'affaires to Tehran and strongly condemned the execution of al-Nimr, who was executed for terrorism offences.

The execution is likely to complicate Saudi Arabia's ­relationship with the Shia-led government in neighbouring Iraq, where the Iraqi Prime Minister Haider al-Abadi is facing calls to close the Saudi diplomatic mission.

Iran's Revolutionary Guards had promised "harsh revenge" against the Saudi Sunni royal dynasty for Saturday's execution of Nimr, considered a terrorist by Riyadh but hailed in Iran as a champion of the rights of Saudi Arabia's marginalised Shi'ite minority.

The protesters gathered in front of the Saudi consulate and chanted slogans against the Arab state's authorities, according to the report.

Around 40 people were arrested.

Al-Nimr's death also drew protests from Shiites around the world, who backed his call for reform and wider political freedom for their sect.

Meanwhile, Mr Nimr's supporters in eastern Saudi Arabia prepared for three days of mourning at a mosque in al-Awamiya in the kingdom's al-Qatif region, following protests on Saturday where police fired tear gas and small shotgun pellets.

Supreme Iranian leader Ali Khameni on Sunday condemned Al-Nimr's execution and threatened Saudi politicians, saying they would pay for it.

And the American State Department said the execution "risks exacerbating sectarian tensions at a time when they urgently need to be reduced".