"We met our deadline last night and all the books have left the warehouse," spokesperson Hope Mokgatlhe said.
The department had an agreement with rights organisation Section 27 that all schools in the province receive textbooks by Wednesday night.
Section 27 spokesperson Mark Heywood said it had only anecdotal reports from the ground, but expected to have a full report from the department at 09:00.
"There certainly was a big effort, and I think many schools will have their books this [Thursday] morning," Heywood said.
"However, we have received contradictory reports as well, therefore we call for an independent verification of the report."
The department of basic education was initially ordered in May to provide Limpopo schools with textbooks by June 15.
The North Gauteng High Court in Pretoria ruled in May that the department's failure to provide textbooks violated the Constitution.
Section 27, which brought the application, met the department after the first deadline expired, and it was decided that delivery of the textbooks be completed by Wednesday.
Meanwhile, the ANC said it was "unfortunate" that Limpopo pupils did not have textbooks in the first half of the year.
"We are saying, it's very unfortunate," African National Congress spokesperson Jackson Mthembu told SAfm.
"Six months into an education year, kids have no books."
However, Mthembu did not want to comment on reports that the department had missed another deadline to deliver the textbooks by midnight on Wednesday.