Other suspects are being sought over the deaths of the two women -- a Dane and a Norwegian -- whose bodies were found on Monday with cuts to their necks, the ministry said.
The bodies were discovered in an isolated mountainous area ten kilometres from the tourist village of Imlil in the High Atlas range.
Imlil is a starting point for trekking and climbing tours of Mount Toukbal, the highest summit in North Africa.
The suspect was arrested in the city of Marrakesh about 60 kilometres north of Imlil, the ministry said.
The Danish victim, Louisa Vesterager Jespersen, 24, "had her throat cut," her mother Helle Petersen was quoted by Danish newspaper B.T. as saying.
Her family had warned her against going to Morocco "because of the chaotic situation," she added.
The other victim was reported by media in Norway to be Maren Ueland, who was 28. She always prioritised safety when travelling, her mother told NRK.
The two women studied together in Norway.
Security was stepped up in the region and hiking suspended following the discovery of the bodies, media said, while the Moroccan interior ministry has confirmed that police are looking for further suspects in connection with the double murder.
Snow and poor weather in the area making investigation of the crime more difficult, local sources told Norwegian media. The two women arrived at Imlil on Sunday, VG reports.
“All of Imlil is in shock. This is a tragedy for the whole town,” a local guide, Mustapha, told the newspaper.
“Nothing like this has happened (here) before),” he said.
The two women are thought to have been sharing a tent. Their bodies were found at the tent on Monday, VG writes. The time of their death is not currently known.
The ambassadors of both Denmark and Norway are to travel to Marrakesh, according to VG's report.
Norway's police security service Kripos has said that it was prepared to assist Morroccan authorities with investigation of the crime, and police in Denmark and Norway were in ongoing communication, the agency's head of communication Alex Due said.
A Norwegian officer in Moroccan capital Rabat is available to assist the investigation.
The Danish Ministry of Foreign Affairs said on Monday that, although it had informed Jespersen's family she was considered to be one of the victims, it had not yet in fact received official confirmation from Moroccan authorities. The ministry did not wish to comment further.