The decision, announced on Wednesday by Israeli officials, would only affect Robertson's Christian group and not other US missionaries, who are growing in ties in supporting the state of Israel.
Abraham Hirchson, the Israeli tourism minister, said he gave instructions to "stop all contact" with groups associated with Robertson.
Last week, Robertson implied that the Israeli prime minister's massive stroke on 4 January was a blow for "dividing God's land" with the withdrawal from Gaza and four West Bank settlements.
But Hirchson said the order did not apply to "all the evangelical community, God forbid".
Robertson is leading a group of evangelicals who have pledged to raise $50 million to build the Christian Heritage Centre in Israel's northern Galilee region, where tradition says Jesus lived and taught.
Under a tentative agreement, Robertson's group was to put up the funding, while Israel would provide land and infrastructure. Hirchson had predicted it would draw up to one million pilgrims a year, generate $1.5 billion in spending and support about 40,000 jobs.
But the fate of the project is now in question, said Ido Hartuv, spokesman for the Tourism Ministry.
"We will not do business with him, only with other evangelicals who don't back these comments," Hartuv said.
"We will do business with other evangelical leaders, friends of Israel, but not with him."
"You read the Bible and he says 'This is my land,' and for any prime minister of Israel who decides he is going to carve it up and give it away, God says, 'No, this is mine'"
In Virginia Beach, Virginia, a spokeswoman for Robertson's ministry declined to comment on Israel's decision.
"We have not talked to the Israelis on this topic," said spokeswoman Angell Watts. "We continue to maintain our long-standing commitment to the Jewish people and the state of Israel."
Robertson's comments on Sharon drew condemnation from other Christian leaders and even George Bush, the US president.
"God considers this land to be his," Robertson said on his TV programme, The 700 Club.
Robertson said: "You read the Bible and he says 'This is my land,' and for any prime minister of Israel who decides he is going to carve it up and give it away, God says, 'No, this is mine'."
The Christian Zionist movement began to take shape in the 19th century, but in recent decades it has strengthened into a powerful force with deep pockets.
These groups consider it their spiritual duty to support Israel as fulfilment of biblical prophecy, and for some as an essential step to bring Judgment Day.
Israeli leaders have seen them as tireless lobbyists in Washington and elsewhere.
The evangelicals have been funnelling millions of dollars each year to Jewish settlers in the West Bank and - before last year's pullout - the Gaza Strip.
US evangelists support Israel
with millions of dollars each year
Some estimates place the annual figure of total evangelical aid to Israel at more than $25 million.
But the Gaza withdrawal has become a new and potent rallying point.
In October, a group of Gaza settlers received a standing ovation from more than 5,000 Christians at Jerusalem conference sponsored by the International Christian Embassy, a private agency that promotes Christian ties Israel.
Robertson's Christian Heritage Center planned for 35 acres of rolling Galilee hills near key Christian sites such as Capernaum, the Mount of the Beatitudes, where tradition says Jesus delivered the Sermon of the Mount, and Tabgha - on the shores of the Sea of Galilee - where Christians believe Jesus performed the miracle of the loaves and fish.
Door still open
Israel was considering leasing the land to the Christians for free.
Hartuv left the door open to continuing the project, but only with people who don't back Robertson's statements.
"We want to see who in the group supports his (Robertson's) statements. Those who support the statements cannot do business with us. Those that publicly support Ariel Sharon's recovery ... are welcome to do business with us," Hartuv said.
"We have to check this very, very carefully," he added.