Hagel's repeated calls demonstrate the degree of US interaction with Egypt's armed forces, even as Egypt reels from deadly protests in the wake of Wednesday's military-backed overthrow of President Mohamed Morsi, the country's first democratically elected president.
The Pentagon said Hagel held three conversations with Egyptian General Abdel Fattah al-Sisi on Friday and Saturday.
"In their conversations, Secretary Hagel emphasized the need for a peaceful civilian transition in Egypt," the Pentagon said in a statement.
"He also noted the importance of security for the Egyptian people, Egypt's neighbors, and the region."
The Pentagon did not comment on Sisi's reaction to the conversations. Details on the combined length of the calls were provided by a US official speaking on condition of anonymity.
The disclosure of the latest conversations came the same day President Barack Obama condemned the violence in Egypt and said that the United States was not aligned with any particular Egyptian political party or group.
Obama, spending the weekend at the Camp David presidential retreat, convened a secure conference call with members of his national security team to discuss events in Egypt days after a military ouster of Morsi and his Muslim Brotherhood-led government.
The Obama administration had grown skeptical of Morsi's ability to lead Egypt. While the United States has expressed concern about the military takeover, it has not condemned it nor called it a coup, prompting speculation that the United States tacitly supports it.