The Verge cited an internal memo which said some of those sacked had occupied the office of its cloud boss Thomas Kurian until they were ejected by law enforcement.
In March, another Google employee was sacked for protesting against the same contract, during a company presentation in Israel.
Protests at the search behemoth against government contracts are not unusual. In May 2018, a dozen employees resigned over Google's involvement in Project Maven, a US Defence Department program designed to use artificial intelligence to interpret video images and assist in targeting enemies in drone strikes.
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The internal Google memo, sent by Google head of global security Chris Rackow on Wednesday, said: "You may have seen reports of protests at some of our offices yesterday. Unfortunately, a number of employees brought the event into our buildings in New York and Sunnyvale.
GOOGLE MOTTOS: A HISTORY
— MGK Hockey 1234 (@mightygodking) 28 March 2018
1999: Don't Be Evil
2003: Try Your Hardest To Not Be Evil
2008: Make A Reasonable Effort To Avoid Being Evil
2013: What Is Evil, Really, When You Get Down To It, I Mean Really
2018: *just a series of high-pitched giggles*
"They took over office spaces, defaced our property, and physically impeded the work of other Googlers. Their behaviour was unacceptable, extremely disruptive, and made co-workers feel threatened.
"We placed employees involved under investigation and cut their access to our systems. Those who refused to leave were arrested by law enforcement and removed from our offices.
"Following investigation, today we terminated the employment of twenty-eight employees found to be involved. We will continue to investigate and take action as needed."
A statement from the group, which calls itself No Tech for Apartheid, described the sackings as a "flagrant act of retaliation".
And it added: "This... is a clear indication that Google values its US$1.2 billion contract with the genocidal Israeli government and military more than its own workers.
"In the three years that we have been organising against Project Nimbus, we have yet to hear from a single executive about our concerns. Google workers have the right to peacefully protest about terms and conditions of our labour. These firings were clearly retaliatory."
Israel has been engaged in military action against the Palestinian extremist group Hamas after the latter killed about 120 Israelis in a raid on 7 October. Since then, Israel has killed more than 30,000 Palestinians, including extremists.