Major General Yisrael Ziv, speaking to reporters on Tuesday, did not say when they were arrested.
"We have in our hands a list of 13 detainees who are to be indicted. They are UN people with suspected links to terrorism," Ziv said.
He gave no details on the jobs or nationalities of those detained.
His comments came after the Israeli army on Tuesday backed away from an accusation that Palestinian fighters had used a UN ambulance to transport a rocket to be fired at Israel, a charge that raised a stir within the world body.
The United Nations, "which is supposed to keep the peace, is cynically used by murderers to transport Qassam rockets in UN vehicles", Israel's UN Ambassador Dan Gillerman had told Israeli radio.
A blurry video taken by a military drone aircraft of the alleged incident has been removed from the army's website amid "an internal discussion of the authenticity of our assessment", a military source said.
"The Israel Defence Forces are reviewing the analysis of the footage in which UNRWA vehicles are seen involved in suspicious activity in the combat zone in Gaza," an army statement said. UNRWA is the UN agency caring for Palestinian refugees.
The video showed men running towards a vehicle with "UN" painted on its roof. One of them carried a long thin object that Israeli officials said was a Qassam rocket but which UNRWA vigorously insisted was a portable stretcher.
"[Israel's] finding is not conclusive, there's now some doubt within the military as to whether it was really a missile or not," a security source said.
"In the footage you see a person lifting the object very easily into the ambulance, which indicates it was not heavy enough to be a missile. We can't say for sure either way yet. An official statement will come in due course," the source said.
Israeli army claimed resistance
fighters were using UN vehicles
A week-old Israeli army offensive into densely populated north Gaza has killed 72 Palestinians, including civilians, and wounded scores. Three Israelis have also died.
The controversy added a chapter to the history of rocky relations between the United Nations and Israel, which sees
the world body as a bastion of anti-Israel bias and is especially suspicious of UNRWA's activities in the West Bank and Gaza.
UN Secretary-General Kofi Annan's spokesman said on Tuesday he would investigate the allegations and ask Gillerman to supply evidence.
Peter Hansen, UNRWA's commissioner-general, demanded an Israeli apology for the allegation, and said his agency's own analysis of the film had established that the object in question was a stretcher, not a missile.
He said it was "appalling" that Israel would spread "false and malicious propaganda", leading its forces to conclude that UNRWA ambulances were "transporting terrorists and weapons".
"[This is] false and malicious propaganda"
Annan's spokesman Fred Eckhard said the secretary-general "has no reason whatever to doubt Hansen's conclusions".
Hansen said on Monday he had no qualms about the fact that some Hamas members figured among UNRWA's many employees.
"Oh, I am sure that there are Hamas members on the UNRWA payroll and I don't see that as a crime," Hansen told Canadian public television, in a reference to the largest Palestinian resistance group.
"Hamas as a political organisation does not mean that every member is a militant, and we do not do political vetting and exclude people from one persuasion as against another."
Hansen stressed that all staff were required to respect "UN standards and norms for neutrality".
Israel has accused UNRWA of ignoring the use of its vehicles and facilities by fighters waging a four-year-old revolt.
UNRWA denies this and accuses Israel of wanton destruction of Palestinian homes, an allegation Israel rejects.