The Egyptian military is resorting to a pungent new tactic to shut down the smuggling tunnels connecting Sinai and Gaza: flooding them with sewage. Along with the stink, the approach is raising new questions about relations between Egypt’s new Islamist leaders and their ideological allies in Hamas who control the Gaza Strip. “Awful,” said Abu Mutair Shalouf, 35, a Palestinian smuggler on the Gaza side, watching workers haul buckets of sewage-soaked soil from the shaft of a tunnel flooded by the Egyptian military 15 days ago. “I don’t know why they did this.”

Advisers to the Egyptian president, Mohamed Morsi, a leader of the Muslim Brotherhood’s political arm, say the answer is simple: they are determined to shut the tunnels to block the destabilizing flow of weapons and militants into Sinai from Gaza — a vow Mr. Morsi made with evident passion in an interview five months ago.

And the more muted response from Hamas, a militant offshoot of the Brotherhood, is the strongest indication yet that its leaders are now pinning their hopes on their ideological allies in Cairo, even if at the moment they appear to be harming the interests of the citizens of Gaza. The tunnels remain a vital source of certain imports to Gaza and smuggling-tax revenue for Hamas, and when the former president, Hosni Mubarak, used far less effective methods to close the tunnels, Hamas screamed of betrayal.

After the sewage flooding, several Hamas officials instead emphasized Egypt’s right to protect its borders as it chose. “Egypt is a state of sovereignty and we do not impose on it anything,” said Salah al-Bardawil, a Hamas official in Gaza. “We address the Egyptian side about the issue and hope they will understand us and our needs,” he added. “We trust the Egyptian leadership that they will not leave the Palestinian people alone.”

Analysts offer many theories about the timing. At a moment of political and economic difficulties, with a financial aid package stalled in the United States Congress, Egypt’s Islamist-led government “is showing itself once more as a valuable ally,” speculated Yasser el-Shimy, Egypt analyst at the International Crisis Group. “It can do something like this, which, perhaps, promotes strategic interests.”

Or perhaps, Mr. Shimy said, Mr. Morsi’s government aimed to remind Israel that it, and not Egypt, still bore responsibility for Gaza’s poverty and problems. Or perhaps the Egyptian military was sending some domestic message of its own, either to the Brotherhood or other domestic constituents, about the generals’ independence from the Islamists.

Concern in Cairo about the tunnels spiked last August, when 16 Egyptian soldiers died in a militant attack on a military outpost in Sinai. The Egyptian government believes the attackers came through the tunnels.

Then, after Egypt helped broker a truce between Hamas and Israel to end a week of fighting in Gaza last November, Israel eased restrictions on imports over the border. Most notably, it began allowing in more construction material previously considered to have a potential military use, though Palestinians say the Israelis still block steel and other materials.

Essam el-Hadded, Mr. Morsi’s national security adviser, suggested this week that the loosened restrictions at the border crossing might have encouraged the crackdown on tunnels. “Now we can say that the borders are open to a good extent — it could still be improved — and the needs of the Gazan people are allowed in,” Mr. Hadded told Reuters.

Under Mr. Mubarak, Palestinians said, the Egyptians sometimes flooded tunnels with gas, which was easily remedied by pumping in air.

But around the beginning of February the Egyptian military began for the first time to use waste water instead, eventually flooding about two dozen of the 200-odd tunnels. (The Egyptian authorities say there are 225; Palestinians say 250.)

Mr. Shalouf, 35, who imported mainly gravel, said that before removing the buckets of dirt he had pumped out the water. Now he plans to lay down sand and sawdust and reinforce the ceiling. Repairs could take three weeks.

Palestinians say that so far the flooding has hurt individual livelihoods but not the total volume of goods moving below ground. On Wednesday, about two cargo trucks per minute were pulling out of the main smuggling zone inside Gaza, laden with cement, gravel, canned food, citrus and vegetables. Hamas customs officers kept a record of each truck and load.