The scratches were discovered after the double-decker plane, the world's biggest passenger aircraft, arrived in Frankfurt on Sunday from New York, SIA said in a statement.
There were 126 passengers and 26 crew onboard.
''The aircraft was subsequently grounded for checks and passengers were either transferred to other airlines or accommodated in hotels,'' the statement said.
''Following inspections by engineering teams in Frankfurt, it was determined that the scratches posed no safety issue and the aircraft was cleared for departure.''
The plane arrived in Singapore on Tuesday after a 23-hour delay and has been grounded for further checks.
SIA said the cause of the scratches has yet to be established.
''Our engineers are currently performing further checks on the aircraft, and it will resume service once cleared,'' the airline said.
It was the second incident for SIA in less than a month involving an Airbus 380.
Last Jan 6, an SIA A380 en route from London to Singapore lost cabin pressure, forcing the pilot to make an emergency landing in the Azerbaijan capital of Baku.
Oxygen masks were activated during the emergency procedure which some passengers described as ''frightening''.
The stranded 467 passengers and 27 crew on board were flown back to Singapore with a replacement aircraft.
The plane involved in the Baku incident was back in service, SIA said Wednesday, but added that the ''root cause'' of the incident remained under investigation.
SIA had previously said that focus of the probe was a door on the main deck that appeared to have suffered a leak, leading to the change in cabin pressure.
There are 119 Airbus A380s in operation globally, according to latest data from the company.
Singapore Airlines currently has a fleet of 19 A380s, with five others on order.
AFP 050511 GMT FEB 14