The case of Sheikh Hussein al-Najati was a stark illustration of the broader mistreatment of Shiites in Bahrain, UN expert Heiner Bielefeldt said in a statement.
He said that he had contacted Bahrain's government to press his "grave concerns" over what he said appeared to be "religiously motivated discrimination" against Najati.
"Targeting the most senior and influential Shia religious figure in Bahrain may amount to intimidating and thus discriminating against the entire Shia Muslim community in the country because of its religious beliefs," he said.
Najati, the Bahrain representative of Iraq-based Shia leader Grand Ayatollah Ali al-Sistani, was among 31 Bahrainis stripped of their citizenship in November 2012 over accusations that they had undermined state security, more than a year after authorities crushed a Shiite uprising in March 2011.
More From This Section
"International law, in particular the Universal Declaration of Human Rights, prohibits arbitrary deprivation of nationality, including on religious grounds," said Bielefeldt, the former head of Germany's national human rights office who took up his UN post in 2010.
The deported cleric arrived in Lebanon yesterday.
"I understand that Mr Najati has consistently refrained from engaging into politics, and has maintained his position and activities strictly in the realm of his religion," said Bielefeldt.
"He is not known to have advocated violence or its use, or to have committed acts that would undermine national security or public order, nor has he been charged or sentenced for committing such acts," he said.
Bahrain remains deeply divided three years after the February 2011 uprising, with persistent protests sparking clashes with police, scores of Shiites jailed on "terror" charges and reconciliation talks deadlocked.