All the incidents involved took place outside of Gaza before the current war.
Israel took corrective action in four units, giving "additional information" on the fifth, the department says.
This means all the units remain eligible for US military assistance.
Washington is Israel's major military backer, supplying it with $3.8bn (£3bn) worth of weapons and defence systems per year.
The announcement is the first determination of its kind for any Israeli unit by the US government.
State Department spokesman Vedant Patel said five security forces units committed gross violations of human rights.
"Four of these units have effectively remediated these violations, which is what we expect partners to do," he said.
"For a remaining unit, we continue to be in consultations and engagements with the government of Israel; they have submitted additional information as it pertains to that unit," he added.
The department denies claims it backed down under political pressure by continuing military assistance to the unit despite being unable to say whether or not there had been any accountability in the case.
"We are engaging with them in a process, and we will make an ultimate decision when it comes to that unit when that process is complete," said Mr Patel.
All the incidents are believed to have taken place in the occupied West Bank and Jerusalem in recent years.
Under America's "Leahy Law", sponsored in 1997 by then-Senator Patrick Leahy, a finding that a foreign military unit committed gross violations of human rights means it can be cut from receiving US military assistance.
The US government says it considers torture, extrajudicial killing, enforced disappearance and rape as such types of violations when implementing the Leahy law.
Even when there is such a finding, there is an exception to cutting military assistance if the state department is satisfied the cases have been dealt with and justice pursued by the government involved.
It says Israel did do this - so-called remediation - in four of the five units. However, the department declined to give any details of the incidents, the remediation, the units involved or evidence to support whether the remediation was effective.
The US was reportedly on the brink of announcing it would cut military aid to the fifth unit, but says new information from Israel means it will make a decision later.
The unit involved is widely reported to be the Netzah Yehuda battalion, a special men-only unit set up in 1999 where ultra-Orthodox Jews serve.
Israel investigated the battalion over the death of 80-year-old Palestinian-American Omar Assad who died after being bound and gagged by soldiers during a West Bank village search in 2022.
At the time the US called for a "thorough criminal investigation and full accountability".
The Israel Defense Forces (IDF) later said they regretted Mr Assad's death, and a commander would be "reprimanded" and two soldiers barred from senior positions for two years - but would not be prosecuted.
Asked about reports an IDF unit would be the first ever to face the US government designation under the Leahy Law, Secretary of State Antony Blinken said on 19 April: "I made determinations. You can expect to see them in the days ahead."
Israeli Prime Minister Benjamin Netanyahu vowed to reject any sanctions on the country's military, saying he would "fight it with all my strength", while Defence Minister Yoav Gallant and war cabinet minister Benny Gantz spoke on the phone to Mr Blinken.
Pressed by the BBC on Monday over whether the state department had delayed or softened its position on withdrawing military assistance to the fifth unit, Mr Patel said officials would make a decision when their consultations with the Israeli government were complete.
By Tom Bateman