Palestinian medics said the three members of the Islamic Jihad group were killed as they approached the border with Israel near the southern Gaza town of Khan Yunis on Tuesday.
A 14-year-old boy also suffered head wounds during an Israeli tank raid, medics said. Several other civilians were also hurt in the fighting.
An army spokesman said three members of Islamic Jihad were carrying large bags and "acting in a suspicious manner".
Israeli tanks also moved into the eastern Gaza Strip overnight where troops seized five Palestinian activists after clashing with fighters there, the army said.
Witnesses said the tanks, supported by unmanned aerial drones, had entered eastern Gaza near the Karni crossing, the main terminal for goods entering and leaving the densely populated strip.
At least three Palestinian fighters in eastern Gaza were also wounded when they were hit by a missile fired by one of the drones.
Hamas members targeted
An army spokesman said the raid in eastern Gaza targeted five wanted Palestinians, including two members of Hamas, which controls the Palestinian government.
Bodies of the Islamic Jihad
fighters are readied for burial
"Forces surrounded a house in which the five wanted Palestinians were located," the spokesman said.
"Some exchanges of fire occurred during which one of the wanted men was injured. The five were arrested and taken for questioning."
The spokesman said weapons were found in the house.
Israeli tanks and bulldozers also entered a village east of Khan Younis on Tuesday morning.
At least two Palestinian civilians were wounded in the clashes, including the 14 -year old, witnesses said.
Israel has carried out repeated brief incursions into Gaza over the past six weeks, since Palestinian fighters captured an Israel soldier.
The Israeli raids also aim to stop Palestinians firing rockets into towns in southern Israel.
Earlier on Tuesday Israeli air strikes targeted houses in Jabalya, a district of Gaza City, in the northern part of the strip, and the southern Gaza town of Rafah, but there were no immediate reports of any casualties or damage.
Witnesses said residents had been warned to leave the buildings ahead of the strikes, which they said appeared to target the homes of members of Hamas and Islamic Jihad, two resistance groups.
Troops entered Gaza in tanks,
supported by unmanned drones
The Israeli army confirmed the airstrikes, saying early on Tuesday that it was targeting arms storage facilities. The army also confirmed that in both cases it had warned residents of the buildings to leave, saying it wanted to avoid civilian causalities.
In the meantime, Egypt deployed 1,300 civilian police officers to beef up security along the Gaza-Egypt border over fears that Palestinian militants might attempt to breach the frontier in order to smuggle weapons into the Gaza Strip.