The MEPs, who include a Catalan politician and representatives from Poland and the Baltic countries, claimed that these stopovers were allegedly "key to maintaining the Russian army's positions in Ukraine."
Also, they asked Mogherini whether the stopovers are in sync with EU sanctions against Moscow which were partly launched as a result of Crimea's reunification with Russia.
El Pais reported that since 2011, more than 50 Russian warships, including submarines, frigates and destroyers, have stopped in Ceuta, "to resupply and let their crews rest."
According to the newspaper, the MEPs' complaint was "triggered by the Heritage Foundation, a conservative US think tank with ties to the Margaret Thatcher Center for Freedom."
"The foundation is a staunch defender of the British presence in Gibraltar, and says that 'Spain's policy of allowing the Russian navy to use Ceuta is hypocritical in relation to its reluctance to allow NATO to [travel directly] between Gibraltar and Spanish ports," El Pais pointed out.
The newspaper quoted diplomatic sources as saying that the Russian warships' visits do not violate the EU sanctions' regime, and that neither the EU nor NATO had ever protested the Spanish policy, which implements it "with complete transparency." The sources also said that the visits involve "routine maritime activities and never military activity."
Meanwhile, the Russian embassy in Madrid has voiced surprise about the fact that "such a common practice as calling into foreign ports" could become a matter of dispute.
"The Russian warships' visits take place after permission is requested, in full compliance with international and domestic legislation," El Pais quoted an embassy spokesman as saying.
The United States and the EU imposed a series of sanctions against Russia in 2014, accusing it of interfering in the conflict between the Kiev government and pro-independence forces in southeastern Ukraine's Donbass region.
Moscow has repeatedly denied the allegations, stressing that it was an instrumental party in negotiating the Minsk agreements aimed at ending hostilities between Kiev and supporters of Donbass independence.