"The military has not interfered or has (not) threatened candidate or voters," Deshapriya said at the end of an inspection tour in the region.
He, however, admitted that his department had received complaints about alleged intimidation by the Army.
"There were complaints but generalised and nothing specific about the complaints," Deshapriya added.
He said the Army could move into areas of election only with his approval where he had to make such a request for deployment through the police chief.
The main Tamil party, TNA, and the opposition JVP have complained that the military was bringing undue pressure on their candidates and activists leading to September 21 polls.
The election is the first in the north since the LTTE's three decades old separatist campaign was militarily defeated in 2009.