The ruling came after Johnson County District Attorney Steve Howe said all copies of key documents needed to support charges of falsifying pregnancy termination reports no longer exist, The Kansas City Star reported Wednesday.
The Kansas Department of Health and Environment destroyed the original records in 2005, the newspaper reported.
Howe said he would still prosecute a remaining 58 misdemeanors charges filed in 2007 by the Johnson County district attorney of the time, Phill Kline.
The misdemeanor charges accuse Planned Parenthood of failing to test fetuses for viability and performing late-term abortions.
Planned Parenthood called the dismissal of the felony charges "a significant victory."
"While additional charges in this case remain, we are pleased the most serious charges have rightfully been dismissed. We are grateful Johnson County taxpayers and Planned Parenthood will no longer waste enormous time and money on these politically-motivated allegations brought by now discredited prosecutor Phill Kline," the organization said in a statement.