The Organization for Security and Co-operation in Europe (OSCE) said that no-one was hurt in the incident at Armyansk.
It was the third time the OSCE has been prevented from entering Crimea, now in the control of pro-Russian forces.
In another development, Russia’s deputy foreign minister has held talks with Ukraine’s ambassador in Moscow.
The foreign ministry gave no details but said the talks on Saturday between deputy minister Grigory Karasin and ambassador Volodymyr Yelchenko were held in an “open atmosphere”.
Also on Saturday, President Barack Obama and his French counterpart Francois Hollande warned of “new measures” against Moscow if it failed to make progress on defusing the crisis in Ukraine.
The French presidency said that, in a phone call, the two leaders insisted on the “need for Russia to withdraw forces sent to Crimea” and “to do everything to allow the deployment of international observers”.
It was not clear what “new measures” could entail.
Witnesses travelling with the OSCE said several shots were fired in the air as a convoy of vehicles approached a checkpoint manned by pro-Russian forces on a road leading from mainland Ukraine into the Crimea peninsula.
An OSCE spokeswoman said that the mission was withdrawing to the nearest big city, Kherson, to decide on its next steps.
The Vienna-based OSCE was invited by Ukraine’s interim government, but Russian separatist authorities in Crimea say it does not have permission to enter the region.
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