In 1569 Fleming became a member of the Privy Council, in 1571 he was made Lord High Admiral and in 1590 Lord High Constable. As the Governor of Finland and Estonia he carried the duties of the highest authority of Finland and Estonia for the Swedish realm, next only to the king. He was a strong supporter of the legitimate king of Sweden and Poland Sigismund Vasa and therefore an enemy of Sigismund's paternal uncle, duke Charles of Sudermania, who had also laid claim to the Swedish throne. He subdued rebels of the Cudgel War in 1596–97. A civil war against Charles was however on the horizon.