The Hercules C-130 plane was flying in bad weather and poor visibility and attempted to land on the runway too late, Spanish news reports said.
The plane overshot the runway by 100 metres and landed in a field. Fire units were on standby, but were not needed. Military officials and journalists accompanying the minister were also unharmed.
Officials at Mostar's airport refused to comment, while Mostar police and the Spanish contingent of the EUFOR told Hina they had no information.
Bono came to Mostar to visit the Spanish contingent of the European Union peacekeepers, which numbers 486 troops.
He is due to continue to Kosovo on Monday and Pakistan on Tuesday, where Spanish peacekeepers are also engaged.