The Israeli air force hit the Hamas-ruled Gaza Strip on Wednesday lightly wounding three people, after Palestinians fired at southern Israel, the military and Gaza security officials said.
Israel also arrested a number of senior Hamas members in the occupied West Bank overnight, including one of its leaders in the territory.
Late on Tuesday, the military said that an undefined "projectile" was fired from Gaza towards southern Israel.
A spokeswoman told AFP that it was "very probably" a rocket but that it was not clear where it hit.
Palestinians in the coastal territory have fired both rockets and mortar rounds into Israel over the past week amid anger over US President Donald Trump's recognition of Jerusalem as its capital.
"In response to the projectile fired from the Gaza Strip at Israel earlier, the Israel air force targeted a Hamas military compound in the southern Gaza Strip," the army said on Wednesday.
Gaza security officials said that aircraft hit a Hamas naval base west of the city of Khan Yunis and open land nearby.
Three Palestinians were lightly wounded in the strikes, the health ministry in Gaza said. No casualties were reported on the Israeli side.
Those arrested overnight included Hassan Yousef, one of the founders of the Islamist movement. He was arrested in Ramallah, a Hamas statement said.
Yousef is a member of the largely defunct Palestinian parliament elected in 2006 and was jailed between 2012 and 2014.
A spokeswoman for Israel's Shin Beth domestic security agency told AFP: "He was arrested because of his involvement in encouraging and directing Hamas activity in the West Bank."
Yousef's son, Mosab Hassan Yousef, gained prominence in recent years after a film was released detailing his spying for Israel, called "The Green Prince."
Yousef disowned his son after he admitted to spying on Hamas for Israel.
Trump's announcement last Wednesday has sparked protests across the Palestinian territories, with four people killed and hundreds wounded in clashes or retaliatory Israeli air strikes so far.