In an interview with PTI, Thowfeek described the actions of the Supreme Court and police as "very disturbing" and said they do not augur well for a "young democracy".
Asked if the Elections Commission (EC) would be able to conform to all the guidelines issued by the Supreme Court for holding polls, Thowfeek said: "I don't know. I will have to discuss it with other members of the Elections Commission.
"This is very unfortunate that the Supreme Court is overriding the Constitution of this country. The Constitution gives the Elections Commission certain authorities and responsibilities but the way the Supreme Court and police services are behaving is very disturbing."
Police said polling was stopped because the EC did not comply with an apex court order to have the voters' rolls endorsed by all the presidential candidates.
While annulling the results of the first round of polling held on September 7, the Supreme Court made it mandatory for the voters' list to be signed by all political parties.
But the Progressive Party of Maldives and Jumhooree Party, which were in the second and third positions in the earlier balloting, did not sign the rolls.
Thowfeek said police blocked EC staff and did not allow them to take election materials out of their office. "They used their forces to not allow us do our duty today and that is why we could not hold the elections as directed by the Supreme Court," he said.