Niyazov appointed Agriculture Minister Esenmyrat Orazgeldyyev to replace Begmyrad Tajiev at the head of Turkmengallaonumleri.
Earlier this month, the Turkmen leader accused agriculture officials of falsifying this year's winter grain sowing statistics and raw cotton output figures.
The official TDH news agency says Niyazov also appointed Saparmurat Ashyrov and Tagaimurat Mammedov as governors of the Dashhowuz and Lebap regions, respectively. Both men were given a six-month probation period.
Their predecessors, Aganyyaz Akyyev and Overdurdy Chashaev, were removed from office for "serious shortcomings" in their work.
Chashaev was demoted. Akyyev's fate is not immediately clear.
TDH says Niyazov also replaced a number of lower-ranking regional officials.