The fresh violence comes two weeks after Israel ended a devastating 22-day offensive in Gaza where more than 1,300 Palestinians were killed.
Both sides have violated unilateral ceasefires which ended the fighting.
Palestinian representatives are in Cairo hoping to reach a lasting ceasefire in Gaza.
The Israeli army said the raid, in the town of Rafah, had targeted gunmen who had fired two mortar bombs that landed in Israel.
Reports say the militants were from the Popular Resistance Committee, a small militant organisation in Gaza.
Israeli Defence Minister Ehud Barak has said Israel does not intend to launch another broad operation in Gaza Strip.
"It is not our intention to have an Operation Cast Lead 2," Mr Barak said in an interview with YNet news website, using the Israeli military codename for its offensive which aimed to curb militant rocket fire.
His comments appeared to clash with statements by Prime Minister Ehud Olmert and Foreign Minister Tzipi Livni. Mr Olmert will step down after Israeli elections on 10 February, while Ms Livni of Kadima is one of Labour leaders Mr Barak's main rivals in the polls.
Opinion polls forecast victory for right-winger Benjamin Netanyahu of Likud.
Israeli planes attacked a Hamas security complex and tunnels under the Gaza-Egypt border on Sunday. There were no reported casualties.
Also on Sunday Palestinian militants fired about a dozen rockets and mortars into southern Israel, wounding two Israeli soldiers and a civilian.
Mr Barak conceded that the attacks had not been launched by members of the Hamas movement which controls Gaza, but said it was incumbent on Hamas to stop attacks.
Critics of Mr Barak, Mr Olmert and Ms Livni said the rocket fire is a blow to their stated aim to "change the rules" in the Gaza Strip.
'Impotence and division'
Palestinian Authority leader Mahmoud Abbas is due to meet Egypt's President Hosni Mubarak in Cairo, as part of efforts to bring about a long term ceasefire in Gaza.
Cairo has been holding separate talks with Israeli officials and Palestinians from both Hamas and Mr Abbas's Fatah party, which runs the Palestinian Authority in the occupied West Bank.
Mr Mubarak wants to negotiate a permanent ceasefire which could lead to Gaza's borders being reopened after an 18-month Israeli blockade.
It would also bring an end to the smuggling of weapons through tunnels in the sandy soil underneath Egypt's borders into Gaza.
Representatives from Hamas are in Cairo, but Mr Abbas has said talks were impossible with anyone who rejected the supremacy of the Palestine Liberation Organisation, which he leads.
This follows a statement last week by the exiled leader of Hamas, Khaled Meshaal, said the PLO "expresses a state of impotence, abuse and is a tool to deepen divisions". Hamas has never been a member of the PLO.
Mr Meshaal is in Tehran, where Iranian state TV reported him thanking President Mahmoud Ahmadinejad for Iran's support in what he called the "victory of Gaza's people" in the war with Israel.
There has been a rift between Fatah and Hamas since Hamas took control of Gaza by force in mid-2007.
Mr Abbas has accused Hamas of having "taken risks with the blood of Palestinians, with their fate, and dreams and aspirations for an independent Palestinian state".
Separately, on Monday the UN relief agency Unrwa said Israel had stopped a convoy of 10 trucks carrying paper and educational materials for its schools in Gaza from entering the Strip.
Israel said Unrwa had not coordinated its attempt to bring in the supplies properly with the Israeli authorities.
Both Israel and Hamas have independently declared ceasefires, but they have been broken several times.
About 1,300 Palestinians and 10 Israeli soldiers were killed in Israel's devastating three-week assault on Gaza. About a third of the Palestinian dead and wounded were civilians, while three Israeli civilians died in rocket attacks.