The temple was discovered by seven local residents who were illegally excavating an area in Al-Badrashee district 40 kilometers to the south of Cairo, minister Mamdouh Damaty said.
The diggers were arrested but later released as the area had not been declared an archaeological site before the recent discovery.
According to the minister, seven stelas, remains of columns and a pink marble statue were discovered by the Antiquities Ministry's staff. Many items had been submerged in water.
Damaty added that the ministry will continue work at the site.
King Thutmose III was the sixth Pharaoh of the Eighteenth Dynasty and ruled Egypt for 54 years. He is considered a military genius by historians and is often referred to as "the Napoleon of Egypt.
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