The Hawks' serious corruption investigating unit on Friday concluded search-and-seizure operations at the Dihlabeng and Maluti-a-Phofung local municipalities in the Free State.
According to a statement, the operation started on Wednesday.
"[The operations] come in the wake of investigations in relation to alleged maladministration, fraud and corruption at the municipalities which is valued at about R56m.
"Several documents which will assist in the ongoing probe were seized from different offices," said Hawks spokesperson Captain S'fiso Nyakane in the statement.
Nyakane said no arrests had been made.
The embattled ANC-led municipalities are among several in the province that face power cuts after running into debt of billions.
Eskom extended the deadline for payment in August.
Dihlabeng municipality owes Eskom R192 972 097.83, while the Maluti-a-Phofung municipality owes Eskom R2 627 895 261.10.
In June, Dihlabeng Mayor Lindiwe Kambule Makhalema was suspended after calling President Cyril Ramaphosa a "sellout" in a closed Facebook group.
In February, the Maluti-a-Phofung municipality was placed under a section 139 (1)(b) intervention.
This followed protests by aggrieved municipal workers over unpaid salaries.
Nyakane would not comment further, saying "any further communication on this matter will be limited pending further investigations".
Attempts to get hold of the municipalities were unsuccessful.