Tensions have escalated in past months, with drones downed and tankers mysteriously attacked in Gulf and nearby waters.
Washington and its Arab allies in the Gulf have accused Tehran of carrying out the tanker attacks, which Tehran denies.
The US has since sought to assemble an international coalition it says is to guarantee freedom of navigation in the Gulf.
Israel has made no official announcement on the operation, although Israeli media have reported a possible role for the Tel Aviv.
Iraq "rejects any participation of forces of the Zionist entity in any military force to secure passage of ships in the Arabian Gulf", Hakim said on Twitter.
"Together, the Gulf states can secure the passage of ships," he said.
He added that "Iraq will work to lower tensions in our region through calm negotiations", while "the presence of Western forces in the region would raise tensions".
Tehran and Washington have been at loggerheads since President Donald Trump unilaterally withdrew the US from a nuclear accord between Iran and world powers in May 2018, reimposing biting sanctions.
If the coalition is formed, each country would provide a military escort for its commercial ships through the Gulf with the support of the US military, which would carry out aerial surveillance and command operations.
Britain has said it will take part, but other European countries have so far kept out, fearing it might harm efforts to reach a negotiated settlement with Iran.
On Thursday, Iran's Defence Minister Amir Hatami said the formation of a US-led flotilla in the Gulf would "increase insecurity" and any Israeli involvement could have "disastrous consequences" for the region.