Judicial sources said the court issued the ruling on Wednesday as part of a retrial over violence between Brotherhood supporters and opponents near the Brotherhood headquarters in the capital Cairo back in 2013.
The rulings are the latest among several trials and retrials of Badie and other big shots of the Brotherhood that ruled the African country before the military, led by incumbent President Abdel Fattah el-Sisi, ousted Morsi following mass protests in 2013.
The court on Wednesday sentenced Badie, Shater and four others to life in prison over violence between Brotherhood supporters and opponents near the headquarters, but acquitted former Parliament Speaker Saad al-Katatny along with a former minister, two prominent Brotherhood figures and two others.
All of the defendants have the right to appeal one final time before the Court of Cassation, Egypt's highest civilian court.
The public prosecution may also appeal the acquittals or the life prison terms that two defendants got instead of death penalty
.The defendants faced charges of inciting violence against the protesters in front of the Brotherhood headquarters, aggravated battery and possession of firearms.
Authorities had referred 18 defendants, including five who remain on the lam, to trial in the case and a ruling was issued in 2015.