The court did not allow public or media access to the hearing, which comes after the Malawi Congress Party (MCP) and the United Transformation Movement (UTM) lodged complaints of alleged fraud in the election.
President Peter Mutharika, leader of the ruling Democratic Progressive Party (DPP), held onto power in the May 21 vote, narrowly defeating Lazarus Chakwera of the MCP.
Briefing reporters outside court, MCP spokesman Eisenhower Mkaka said the court was deliberating on how the case would proceed.
Judges heard applications on media access, disclosure of financial documents and where ballot papers should be securely stored.
When the court met last week, police used tear gas to disperse opposition supporters gathered outside.
Security forces were deployed around the court on Wednesday, but there were no protests. Chakwera alleges he was the rightful winner of the election, which he lost by 159,000 votes.
After the result was announced, he described it as “daylight robbery.” Further protests are scheduled for next week.