One of the men acted as the celebrant, who allegedly called the couple "infidels" during the luxury ceremony.
A video of the ceremony was posted on YouTube and went viral, sparking fears for the tourism-dependent economy.
President Mohamed Nasheed has promised new guidelines on conducting wedding ceremonies for tourists.
In his weekly radio address on Friday, President Nasheed described the behaviour of those involved as "absolutely disgraceful".
He said all tourist hotels will be required to follow the rules, which will be issued soon.
He noted that "bad behaviour, such as that depicted in the YouTube video, can cause enormous damage to the country's tourism industry".
The government has launched an investigation into the incident at the Vilu Reef resort.
Both men are being held in police custody while the prosecutor's office decides on charges.
With police refusing to confirm the couple's nationality, their identity remains a mystery, although a Maldives tourism official told AFP news agency they were French.
The foreign ministry identified them as Swiss, however.
The amateur film on YouTube shows a celebrant explaining the ceremony in English before everyone stands and holds their hands up to pray.
'Infidel and atheist'
He uses the intonating style of prayers to unleash a torrent of abuse in the Dhivehi tongue on the unwitting couple, who smile shyly.
"Your marriage is not a valid one," he says. "You are not the kind of people who can have a valid marriage. One of you is an infidel.
"The other, too, is an infidel - and we have reason to believe - an atheist, who does not even believe in an infidel religion.
"You fornicate and make a lot of children. You drink and you eat pork."
The celebrant also makes references to bestiality, sexual diseases and "frequent fornication by homosexuals".
After the ceremony, the couple are taken to plant a coconut tree together, during which various comments are made about the bride's breasts.
The hotel has apologised for the incident and is in contact with the couple to offer compensation, said Ahmed Shakir, the head of Sun Investments, which operates the resort.
He told the BBC he did not know if other couples have been subjected to the same sham ceremony and abuse but the company was investigating the possibility.
Vilu Reef charges $1,300 (£820) for the ceremony, which it says offers couples the chance to "mark a milestone in your amazing journey together".
The full video on Youtube
Basically, a couple goes to an island paradise to get married, the guy conducting the marriage ceremony doesn't like foreigners/non-muslims/perceived-amorality/whatever, insults the couple in his own language, and pretends it's a religious prayer. All while accepting their money for the services. Apparently the priest (or whatever) didn't realize that someone on the interblags might be able translate, and it caused a huge emberassment in a country whose chief export is tourism.
Reminds me of that case where the tattoo artist, tired of preppy white kids getting Chinese/Japanese letter tattoos that they couldn't even read, decided to simply tattoo insults on them. Oh, and in prison he later tattooed insults on the inmates, and had to be placed in a private cell for his own safety.