Spanish Prime Minister Pedro Sanchez said on Monday that Moroccan naval vessels entered Spanish waters off Ceuta without permission after late July's mass migrant crossing into the North African enclave, state broadcaster TVE reported.
He downplayed the incidents as isolated and underscored the importance of relations with Morocco.
At the end of July, over 72,000 migrants crossed the border from Morocco into Ceuta, sparking a humanitarian and diplomatic crisis, which remains partially unresolved, stoking political tensions in Spain as it prepares for an early election on 29 November.
El País newspaper reported on Monday, citing unnamed sources, that following the border rush, at least one frigate and several patrol boats from the Royal Moroccan Navy sailed through Spanish sovereign waters without seeking authorisation.
A Spanish frigate had to intercept Moroccan warships to repel them from Spanish waters, it said.
"We must acknowledge that, between two neighbouring countries, such isolated incidents do occur," TVE quoted Sanchez as saying. It did not quote Sanchez addressing the specifics of the El País report.
"We are neighbours. Those were intense days, but cooperation between the navies remains smooth, regardless of that incident," he added, saying relations with Morocco are "very important".
The comments came on the eve of a visit by King Felipe and Queen Letizia to Ceuta on Tuesday and Wednesday, which could heighten tensions between Spain and Morocco. Rabat claims sovereignty over Ceuta and Spain's other enclave, Melilla.
The government did not reply to a Reuters request for comment. The Moroccan foreign ministry could not be immediately reached for comment.
On Friday, Morocco's King Mohammed said the cooperation model with Spain on migration had reached its limits, criticising Spanish court decisions impeding the repatriation of minors and asylum seekers as "obsolete".
While most migrants returned in the weeks after the crossing, thousands remained.