The decision was taken in response to the Gaza flotilla incident, he said.
"At times where we are focused on humanitarian aspects… we cannot talk about commercial and economic matters," the minister said.
The projects suspended include a water initiative that was to see Israel receive water from Turkey, as well as a natural gas pipeline to Israel. However, the boycott does not include transactions involving non-governmental companies, the minister said.
The Turkish response is also expected to affect security and defense cooperation between the countries on the economic front.
"Officials at our defense industries and in the Defense Ministry already realize that in the near future there will be no significant contracts with the Turkish Defense Ministry," a defense official told Calcalist earlier this week.
Meanwhile, the Turkish finance minister on Thursday said he was not worried about Turkey's economy being harmed by the deteriorated relations with Israel.
"I don't think that we would see a major impact from the Israeli incident," Mehmet Simsek said in a press conference following a convention on global recession and it effects on the Turkish economy.
"We will be receiving maybe twice as many as tourists from the Middle Eastern countries than we expect to receive from Israel. Besides, Israel's share in Turkey's economy is minimal – around one percent – as for in tourism, bilateral trade or in foreign direct investments," he said.
"Relations between Turkey and Israel would never be the same again. Israel will have to face the consequences of its actions," he added.