Ex-Samoa hooker Schwalger, 46, had been suspended since September after being charged with sexual misconduct with a person aged under 16.
"Mase has given everything to our country through the Manu Samoa, and his contributions to the team and our rugby community will always be acknowledged," Lakapi Samoa president Sailele Malielegaoi said in a statement.
"His leadership has been a key part of our journey," he added.
Former Scarlets and Sale front-rower Schwalger had been appointed in April.
"The resignation follows a period of suspension granted to Mase following the filing of criminal charges against him in court," Lakapi Samoa said.
Lakapi Samoa said a search for a new head coach will start with the sport in the country in turmoil.
They were forced to withdraw fromm three Tests in November due to severe financial issues.
Experienced Samoa prop Paul Alo-Emile told AFP in November he was unsure whether he would continue to play for the side amid the off-field problems.
