"This partnership faces a continuous judicial harassment and repeated media attacks," Bourita told reporters following talks with EU foreign policy chief Josep Borrell, although Bourita did not directly refer to the cash-for-influence case.
"This partnership faces attacks in European institutions, notably at the parliament," Bourita added.
Belgian authorities have charged four people linked to the European Parliament over allegations that Qatar lavished them with cash and gifts to influence decision-making. Qatar has said it had no involvement in the scandal.
In arrest warrants issued in Italy, there are also allegations of payments from Morocco.
Morocco has not publicly comment on the case.
Morocco's partnership with the EU is "based on neighbourliness, values and mutual interests," said Bourita.
The graft accusations "are grave", Borrell said after discussing the issue with Bourita and earlier in the day with Prime Minister Aziz Akhnnouch. Borrell gave no details.
The European Union maintains a position of "zero tolerance" of corruption and will wait for the results of the decision of a judicial investigation into the case, he said.
Separately, Borrel said the EU and Morocco had a "solid strategic partnership."
He said EU aid to Morocco would increase to 1.6 billion euros during 2021-2027 from 1.4 billion in 2014-2020.
(Reporting by Ahmed Eljechtimi, Editing by William Maclean)
