This major river originates in India but was allocated to Pakistan under the 1960 Indus Waters Treaty, signed by the two nuclear powers.
India suspended the treaty following a deadly attack in Indian-administered Kashmir on April 22 that killed 26 people.
Islamabad warned that tampering with its rivers would be considered "an act of war".
"We have witnessed changes in the river (Chenab) which are not natural at all," Kazim Pirzada, irrigation minister for Punjab province, told AFP.
Punjab, bordering India and home to nearly half of Pakistan's 240 million citizens, is the country's agricultural heartland, and "the majority impact will be felt in areas which have fewer alternate water routes," Pirzada warned.
"One day the river had normal inflow and the next day it was greatly reduced," Pirzada added.
In Pakistan-administered Kashmir, large quantities of water from India were reportedly released on April 26, according to the Jinnah Institute, a think tank led by a former Pakistani climate change minister.
"This is being done so that we don't get to utilise the water," Pirzada added.
The gates of the sluice spillways on the Baglihar dam in Indian-administered Kashmir which lies upstream of Pakistani Punjab "have been lowered to restrict water flow ... as a short-term punitive action", a senior Indian official has told The Indian Express.
The Indus Waters Treaty permits India to use shared rivers for dams or irrigation but prohibits diverting watercourses or altering downstream volumes.
Indian authorities have not commented yet but Kushvinder Vohra, former head of India's Central Water Commission, told The Times of India: "Since the treaty is on pause... we may do flushing on any project without any obligation".
Experts said the water cannot be stopped in the longer term, and that India can only regulate timings of when it releases flows.
However, the Jinnah Institute warned: "Even small changes in the timing of water releases can disrupt sowing calendars (and) reduce crop yields".
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