It indicated serious damage was likely to be caused to buildings and roads, and that people should avoid travelling unless absolutely necessary.
In Ras Al Khaimah, the towns of Munai and Wadi Sa’am were both hit hard by sudden downpours.
Rainwater swept through the areas at speed, washing away embankments, felling trees and damaging property.
Meanwhile in the capital, footage showed water pouring through the dome-shaped roof of Louvre Abu Dhabi.
Several large trees around the Sheikh Zayed Grand Mosque in the capital were also uprooted by ferocious gusts of wind.
In a further incident, a crane was ripped from its mooring on a construction site in the city before falling on to a neighbouring high-rise.
And in Sharjah, emergency services were called out to rescue a school bus trapped by the flooding.
On Monday, road maintenance teams and street sweepers were out in force across the country assisting with the clean-up.
Debris from the heavy rain and subsequent flooding, including roots and branches of trees as well as construction materials, was strewn over areas of Abu Dhabi, Dubai and the Northern Emirates.