"Give Iran a space," Sheikh Mohammed said in an interview with the BBC, excerpts of which were provided by the channel today.
He said he was in favour of the lifting of sanctions slapped on Tehran over its controversial nuclear programme, in the wake of a landmark deal on the issue reached with world powers.
"Iran is our neighbour and we don't want any problem... lift the sanctions and everyone will benefit," Sheikh Mohammed said.
The sheikh said he believes that Tehran is "telling the truth" when it says that its nuclear ambitions are peaceful.
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Being a hub for transit trade, Dubai's commerce with Iran was hit by the tightened sanctions. The city has an Iranian community of around 400,000 people.
Tehran signed in November a landmark deal with world powers under which it agreed to roll back parts of its nuclear work and halt further advances in exchange for the release of billions of dollars in frozen assets and limited relief from sanctions that have choked its economy.