The country previously backtracked on lifting a hunting ban on the species, recognisable by their long, trunk-like rounded snout.
President Kassym-Jomart Tokayev had called the antelopes "sacred animals for the Kazakh people". The saiga was massively poached in the 1990s.
State media cited Kazakhstan's deputy minister of ecology as saying the decision to hunt them was "necessary due to the rapid growth of their population" and "complaints from farmers".
A spokeswoman for Kazakhstan's ecology ministry told AFP Wednesday that "according to scientific research, it is possible to eliminate up to 20 percent of the total population without harming the species".
The exact number of animals allowed to be culled and the start date of the hunt are yet to be determined, she added.
Farmers complain that saigas have stomped thousands of square kilometres of farms, where crops are also threatened by climate change.
According to the latest estimates, there are 4.1 million saigas in the former Soviet republic, representing almost the entire global population, a number that could rise to five million by the end of the year.
An attempt to lift the ban was met with opposition in 2023, a rare occurrence in Kazakhstan, where freedom of expression is limited. The authorities reversed the decision a few months later.
Poaching of the antelopes exploded after the collapse of the Soviet Union, particularly as their horns are used in traditional medicine.
Water shortages and disease had also endangered the species before the Kazakh authorities introduced a policy to protect them.
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