Mexico's Foreign Relations Department said in a statement late Tuesday that search crews from the two nations have been combing both sides of the border near the town of Ojinaga, across the border from Presidio, Texas.
"Unfortunately... the search has not yielded any results," the department said.
It said the swelling of the Conchos and Bravo rivers have made the search difficult.
Earlier Tuesday, Chihuahua state Gov. Jose Reyes Baeza Reyes told reporters in Ojinaga that U.S. investigators had located the plane and that all four passengers had died in a crash. His press office later retracted his statement and said the search for the plane continued.
The plane carried U.S. commissioner Carlos Marin and his Mexican counterpart, Arturo Herrera. Jake Brisbin Jr., executive director of the Rio Grande Council of Governments, also was on the plane along with a pilot, according to Presidio County Judge Jerry Agen.
Sally Spener, a spokeswoman for the IBWC in El Paso, said the plane left El Paso just after 10 a.m. Monday and was scheduled to pass over the Luis Leon Reservoir in northern Mexico so the men could get a view of floodwaters that are threatening levees on both sides of the border near Presidio.
Officials started looking for the plane Monday after it didn't land as scheduled in Presidio, about 250 miles southeast of El Paso.
Marin has worked with the IBWC's U.S. section since 1997. He was appointed interim commissioner in 2005 and took the title permanently a year later on an appointment from President Bush.
Herrera has led the Mexican section of the IBWC for more than 18 years.
The international agency is responsible for maintaining the border between the U.S. and Mexico. In areas divided by the Rio Grande, that includes building and maintaining levees.
Ongoing flooding has prompted the evacuations of hundreds of people living on both sides of the swollen river.
Spener said Tuesday that a levee along the Rio Conchos, a river that feeds into the Rio Grande, failed Monday night. Floodwaters were reported in low-lying areas on the western side of Ojinaga. Monday afternoon, houses and businesses near the Rio Grande levee in the Mexican border city were lined with sandbags and appeared empty.
"We understand it (the levee break) is affecting low lying areas in Ojinaga," Spener said. "That did relieve some of the flows that have been in the Rio Grande but we do expect that water levels will rise."