"The government of Pakistan has not invited the Israeli agriculture minister," foreign ministry spokesman Masud Khan said.
Katz told Israeli military radio he had been "officially invited to go to Pakistan" as part of a United Nations agricultural delegation and that he had accepted.
Khan said the United Nations Food and Agricultural Organisation (FAO) had suggested sending a delegation to Pakistan in March for a conference on crop maximisation, but had given no details on who would be in the delegation.
Islamabad told the FAO that March was not suitable.
Pakistan is a Muslim country with which Israel does not have diplomatic relations.
An Israeli press report had said a visit by an Israeli minister to Pakistan could herald the start of diplomatic relations between the two states.
"I have been officially invited to go to Pakistan during the month of March and I have accepted," Katz said, adding that the visit "will take place in the framework of a UN delegation" of officials in charge of farm matters.
"I have been officially invited to go to Pakistan during the month of March and I have accepted. The visit will take place in the framework of a UN delegation"
Israeli agriculture minister
"This visit reflects a rapprochement between the two countries, it is an important visit as Pakistan is a Muslim atomic power," the minister said.
Katz added: "Pakistan, India and Israel are with the Americans on the same side in the fight against terrorism."
The Israeli daily Maariv newspaper said the announcement had been preceded by several secret meetings between officials of the two countries in recent months.
President Pervez Musharraf of Pakistan could meet Israel's foreign minister, Sylvan Shalom, at the upcoming World Economic Forum in Davos, Switzerland, the paper added.
Maariv said the reported contacts between the two countries had taken place both in Europe and the United States.