"A number of Lebanese residents have been deported after it was confirmed that they belonged to and supported terrorist Hezbollah," the ministry said in a statement posted on its Twitter account.
The ministry did not provide any further details, including on the number of people involved. Lebanese press reported last week that up to 10 families had been ordered to leave Bahrain within 24 hours.
The move comes a day after Bahrain's neighbour Saudi Arabia warned that it will punish citizens and residents who "support or demonstrate belonging" to Hezbollah.
In January, Bahrain said it had dismantled a "terror" cell allegedly linked to Iran's Revolutionary Guards and Hezbollah.
Shiite-majority Bahrain, which is ruled by the Sunni Al-Khalifa dynasty, has repeatedly accused Iran of meddling in its affairs, a charge categorically denied by Tehran.