Margallo insisted that Spain had not closed its airspace to Morales as he travelled from Moscow, Russia, to La Paz, Bolivia, nor endangered his life.
The Bolivian president's plane was eventually forced to land in Vienna, Austria, where it was detained for 13 hours.
The incident was the result of a rumour that fugitive American 'IT Spy' Edward Snowden was also travelling on board, according to Spanish daily El País.
Snowden is currently holed up at Moscow airport seeking to avoid US espionage charges after leaking embarrassing details of a vast US phone and Internet surveillance programme.
Morales had been in Russia at an energy conference and was returning home to Bolivia when his flight was diverted to Austria.
Margallo said, "if there has been any misunderstanding then naturally we will say that we are sorry."
The foreign minister's words represent a step back from Spain's stance at last week's Union of South American Nations meeting when Margallo declared that the country had nothing to apologize for.