There have been anti-semitic protests recently about the transport ministry's decision to allow direct flights from Israel, while a restaurant that hung up Christmas decorations in 2010 was also targeted, the report said.
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"We found that they are perfectly healthy and places where families can obtain top class treatment," Maldives President Nasheed was quoted as saying by AFP, a news agency.
"We feel comfortable that we can now open the spas.
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The spas were closed following protests by a hardline opposition party.
The tourism industry in the Maldives had also sought the intervention of the Supreme Court to lift the ban, saying it was unnecessary and would deprive them of business, the report said.
The Indian Ocean country last year received more than 850,000 tourists, but its reputation as a "laid-back holiday paradise" has been hurt by religious fundamentalists, the report said.