Party officials told the electoral office they have been contacted by 18 people whose votes had been "stolen".
The Chief Electoral Officer said she is investigating 12 allegations of electoral fraud in the Foyle constituency.
Former SDLP leader Mark Durkan lost the seat by 169 votes to former city lord mayor Elisha McCallion of Sinn FÃ©in.
The police have said they are investigating a small number of reports of electoral fraud, following an Electoral Office referral.
Chief Electoral Officer Virginia McVeigh said:  "The investigation is at a very early stage. We have made a number of calls for other people to come forward."
The SDLP said about a dozen incidents of voter fraud had also been reported in South Down and has called for tighter controls on voter identification.
SDLP veteran Margaret Ritchie was defeated in South Down by Sinn Fein's Chris Hazzard by 2,446 votes.
SDLP MLA Mark H Durkan said he had been contacted by people who were told they had already voted when they arrived at polling stations.
"It's difficult to gauge how widespread it may be," said Mr Durkan, the nephew of the defeated Foyle MP.
"It is horrifying to think that in this day and age that voting fraud is going on.
"It is vitally important to all parties that we have an electoral system that people can have faith and confidence in."
BBC News NI political correspondent Enda McClafferty said:  "While allegations of voter fraud are not new, the SDLP claims it is more of a problem now - especially in constituencies like Foyle where only 169 votes separated the winner and loser."
No accusations have been made against any one party but in response to the SDLP claims,  Sinn FÃ©in said there was always an effort by political opponents to explain away their rejection by the electorate.
Police have asked anyone with concerns about electoral fraud to contact the Electoral Office.
Ch Supt Karen Baxter said: "We work closely with the Electoral Office and where information becomes available in relation to criminal activity, we take action."
Police are investigating allegations of electoral fraud amid concerns raised by the SDLP in the Foyle constituency.