The minister warned that Irish passport holders would be less welcome in countries as a result of five of the assassination squad using fraudulent Irish passports.
Mr Martin said he had already received a report of an Irish businessman who had experienced “very negative treatment” in Dubai because of the perception Ireland was involved in the killing.
The use of forged Irish passports put the security of Irish citizens at risk and violated the integrity of our passport system, the minister said.
Mr Martin met his Israeli counterpart, Avigdor Lieberman, in Brussels and told him he was gravely concerned about the fraudulent use of Irish passports.
Mr Lieberman, who met him in the Irish embassy while on a visit to the EU, told Mr Martin he did not have any information about the incident.
The Dubai authorities have claimed the Israeli spy agency, Mossad, was responsible for killing Mahmoud al-Mabhouh on January 20.
Mr Martin said the passport numbers used were not from the new biometric passports, but said the theft of the identities of five Irish people had serious implications, such as their being added to the list of terror suspects.
“If they were travelling at the weekend they would have been in significant difficulties with security authorities”, the minister said.
He added that the UAE foreign minister told him when they spoke at the weekend that EU nationals could face more difficulties getting into his country in the future as a result.
The Garda have been working with investigators in the United Arab Emirates and in other EU countries. UAE Foreign Minister Sheikh Abdullah bin Zayed al-Nahayan told him on Saturday evening that they have done a lot of investigative work tracking the documents and how the assassination was planned.
British foreign secretary David Miliband also met Mr Lieberman. Eight British passports were used, all using the identity and photographs of British citizens living in Israel. There was one forged French and one German passport also used.
The EU’s foreign ministers issued a statement after discussing the issue at their monthly meeting yesterday, condemning the killing and the use of stolen passport identities.
However, Israel was not named and the language was toned down at the request of a number of countries including Germany and the Netherlands.
The incident has sparked a major diplomatic row between Israel and the European countries in question.