The strongest storm on record to reach Nicaragua, Iota struck the coast late on Monday, bringing winds of nearly 155 miles per hour (249 kph) and flooding villages still reeling from the impact of Hurricane Eta two weeks ago.
Iota was drenching already saturated towns and villages as it moved inland over southern Honduras and as authorities reported many people missing with some of the worst-hit areas still cut off.
The Honduran government closed bridges and highways across the country on Tuesday, while opening more than 600 shelters where some 13,000 residents sought refuge.
Nicaraguan Vice President Rosario Murillo said at least six people had died as they were dragged down by raging rivers.
The double punch of Eta and Iota marked the first time two major hurricanes had formed in the Atlantic basin in November since records began. The Nicaraguan port of Puerto Cabezas, still partly flooded and strewn with debris left by Eta, again bore the brunt of the hit.