GAZA —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.