While Guzman paced back and forth several times between the bathroom area and his bed before vanishing, National Security Commissioner Monte Alejandro Rubido said it was common behavior for prison inmates.
The small hole on the shower floor that Guzman, 58, slipped into for his daring escape late Saturday is not seen in the footage.
While a surveillance camera was on a corner outside the cell and another inside pointing toward the shower, authorities said they had two blind spots to protect the inmate's privacy.
Guzman's second escape from a maximum-security prison in 14 years is a huge embarrassment to President Enrique Pena Nieto's administration, which had celebrated the capture of the world's most wanted drug baron just 17 months ago.