Among other places the rain lashed Chandigarh, Mohali, Ropar, Ludhiana, Patiala, Hoshiarpur, Panchkula, Kurukshetra and Kalka.
The local Meteorological Department has forecast more rains at few places in the two states until tomorrow.
The wheat procurement is set to begin soon and if heavy rains or hailstorm occur at this stage, they can be damaging, Punjab Mandi Board President Ajmer Singh Lakhowal said.
Bharatiya Kisan Union (Rajewal) President B S Rajewal said that farmers in the two states were praying and keeping their fingers crossed in the hope that it does not rain.
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A farmer from Kurukshetra said that the farmers were hoping the weather holds good otherwise it can damage their wheat crop.
Lakhowal, who is also President of BKU (Lakhowal), said "if the weather does not play spoilsport, overall, we don't see much impact, as the government has made all necessary arrangements for procuring record 140 lakh tonne of wheat, which we are expecting during rabi marketing 2013-14 season starting April 1".
Meanwhile, a MeT official said that current change in the weather was due to a Western Disturbance over North Pakistan and adjoining J&K.
The maximum temperatures in the plains of Punjab and Haryana have been settling in the range of 26-29 degrees Celsius during the past few days, which is 2-3 degrees below normal level.
The days will be partly cloudy in Haryana and Punjab and light rain or thunder showers may occur at some places followed by thunder squalls with wind speed exceeding 45 kmph at isolated places.