In a statement Friday, the ministry said the publishers of seven government-approved textbooks had been ordered to revise 41 instances of "obscure and unbalanced" descriptions of history.
Failure to do so would result in publication of the books being halted completely, the ministry said.
The 41 corrections demanded by the ministry involved writings on subjects ranging from civilian killings during the 1950-53 Korean War, territorial disputes with Japan and North Korean human rights abuses.
"The most important factors for determining the subjects of modification were if there are any factual errors and elements that could negatively affect students' perspective of the right historical events," Deputy Education Minister Na Seung-Il told reporters Friday.
The directive follows a row that was triggered in August by protests from liberal opposition lawmakers over one particular textbook which they accused of a pronounced right-wing bias.
Ruling conservative MPs countered by challenging a perceived left-wing bias in a handful of other textbooks.
The turbulent, traumatic history of the Korean peninsula in the 20th century is something of an academic minefield.
Of particular sensitivity are the 1910-45 period of Japanese occupation, the division of the peninsula into North and South, post-Korean War military rule, the pro-democracy movement of the 1980s and 1990s, and pretty much anything to do with North Korea.
The left-right divide in South Korea still battles over the portrayal and legacy of all these subjects, which remain a critical part of the national consciousness.
High school textbooks have been a proxy battlefield for these ideological forces before, most recently in 2004 when conservatives took exception to a perceived left-leaning publication.