Several thousand Gaza Strip residents have attempted to cross into Egypt after being given a rare opportunity to leave the area that has been blockaded for the past three years.

Egypt temporarily opened the Rafah border crossing, so that aid materials could be delivered in the wake of Israel's controversial raid on a Gaza-bound aid flotilla.

Murad Muwafi, the governor of Egypt's northern Sinai district, said the gesture was meant to "alleviate the suffering of our Palestinian brothers after the Israeli attack."

That prompted Gazans to rush to the border, many carrying overstuffed suitcases and bags along with them.

Ihab Ghussein, a spokesperson for the Hamas Interior Ministry, said "we are working to help residents take advantage of this opportunity. We hope it will be open all the time, not just as a response to yesterday's events."

However, after hours of waiting, many were sent home by Hamas security forces.

Meanwhile, the Israeli military killed three members of an Islamic militant group during a Tuesday air strike in Gaza. Two other militants were killed in a separate incident as they crossed into Israel.

In Jerusalem, the Israeli government remained on the defensive after the disastrous Monday morning raid killed nine activists riding in a six-ship flotilla.

Miriam Ziv, Israel's ambassador to Canada, said Tuesday that her government will not consider lifting the Gaza blockade while it has concerns about arms smuggling into the region.

Ziv said Israel was prepared to accept humanitarian aid through the Port of Ashdod, but the organizers were instead keen on trying to break the blockade.

"We could not change our position and we will not change our position," Ziv told CTV's Power Play Tuesday evening. "We have to make sure that no other goods but humanitarian aid goes into Gaza, and the only way to do it is through the passage that we are allowing for it to go, and not through sea because the smuggling into Gaza of arms is a problem."

While the six ships were detained by Israel, the cargo was searched and much of the aid has since been transferred into Gaza by land, Ziv said.

Many Israeli citizens and members of the national media have asked questions about the level of preparation military officials undertook when planning the raid.

"The entire intelligence community had all the time it needed to follow the protesters' plans and preparation. Drones provided constant streaming videos of the ships, and it's safe to assume other means of tracing and sabotage were used: Signal jamming, signal tapping, possibly even live agents," said retired general Shlomo Brom.

"And still, based on the commandos' testimonies yesterday, it's clear they were not prepared for what awaited them on the deck."

UN calls for investigation into raid

The UN Security Council called for a "prompt, impartial, credible and transparent investigation" and reiterated its desire to see a regular flow of goods and people into Gaza.

A number of envoys said Tuesday Israel is violating international law. They pointed to UN Security Council resolution 1860, passed in January 2009, which calls for an end to the Gaza blockade and to allow the unimpeded flow of aid into the region.

In addition to facing international condemnation Tuesday, the Israeli government was also dealing with the influx of 679 activists who were arrested after Monday's raid. The Israeli government announced late Tuesday that nearly all of them will be deported within the next two days. However, about 50 will be held for further investigation.

"It's clear that we have to investigate each one of them, find out who they are, what their intentions are," Ziv said.

"I actually think that many of them were really sincere peace-loving people who wanted to supply aid to Gaza…But it is clear that there was a group on this boat that was there in order to instigate violence, they were actually baiting the Israelis and created this situation."

Turkish citizen Nilufer Cetin was one of the people who took part of the flotilla and who returned home Tuesday after being deported.

Cetin told reporters "there was a massacre on board" that turned the ship "into a lake of blood."

Also Tuesday, the Free Gaza Movement, which organized the flotilla, said two more ships will make their way towards Gaza -- one is already en route from Italy, the other is set to join it.

"This initiative is not going to stop," spokesperson Greta Berlin said Tuesday.

"We think eventually Israel will get some kind of common sense. They're going to have to stop the blockade of Gaza, and one of the ways to do this is for us to continue to send the boats."

The two boats are expected to arrive in the region late this week or early next week, Berlin said.

With files from The Associated Press