Janez Drobnic, minister in charge of family, labor and social welfare, refused Jansa's request to step down earlier in the day, saying that he did his job properly.
"I won't resign," he said, leaving Jansa no choice but to seek his ouster through parliament, which has the final say in appointing and firing ministers.
Jansa said Thursday that Drobnic's proposals "caused conflicts," and that he had failed to competently run the ministry.
Jansa did not specifically mention the abortion issue, but Drobnic has faced harsh public criticism for the past 10 days after proposing that women seeking abortion pay for the procedure, now covered by the country's health care system up to the 10th week of pregnancy.
It was not immediately clear when parliament could debate and vote on Drobnic.
Drobnic is a member of the Nova Slovenija Party, a junior partner in Jansa's center-right coalition, which came to power two years ago.
Drobnic's proposal on abortions was part of a larger plan to reverse the declining birthrate of this nation of 2 million. It had not yet been discussed by the Cabinet.
Drobnic argued the measure would prompt women seeking abortions to change their minds, reports AP.
His plan, which was supported by the country's Catholic Church, still allows abortions free of charge if performed for medical reasons.
Feminist groups, prominent intellectuals and doctors protested the plan, claiming it would only result in women seeking to have abortions illegally. Opponents also say the number of abortions in Slovenia a predominantly Roman Catholic country has dropped anyway.
In a recent survey carried by the leading daily Delo, 75 percent of those interviewed opposed Drobnic's idea.