Police Scotland were called to investigate at the end of June when Annan Athletic failed to receive an end of season payment from the league.
The League Two side were expecting about £18,000 but the funds were paid into a fraudulent account.
BBC Scotland has learned that the money has been retrieved and that the police investigation continues.
The SPFL said it has been subject to further attempts at hacking and fraudulent activity as recently as this week.

The device was found at Corfe Mullen, Dorset on Tuesday morning.
A Military Explosive Ordnance Disposal team (EOD) has set up a 1,000m (0.62 mile) exclusion zone at Henbury Quarry in Old Market Road, ahead of a controlled explosion at 10:00 GMT.
Local roads within the cordon and the A350 will be closed from 09:30.
Superintendent Caroline Naughton, of Dorset Police, said: "I would like to reassure residents that there is no immediate risk to anyone in the local area.
"When the controlled explosion takes place it is anticipated that a loud bang will be heard in the area."
A rest centre has been set up for residents at the Memorial Hall, Sturminster Marshall.
People are being urged to take any pets or medication with them.
Dorset Police said staff and pupils from Castle Court School are being taken to another site.
The cordon is expected to be lifted by 11:00 GMT.

The fire blew out the windows of the property on Lewes Road, initially leading to reports that there had been an explosion.
Emergency services attended the scene at 02:50 BST and the body was discovered in the upstairs of the house, which had been badly damaged.
Police and the fire service are carrying out a joint investigation into the cause of the fire.
Residents from several neighbouring homes, which were evacuated, have now been allowed back into their properties.
The street, just off Neasham Road, remains cordoned off.

The officer was carrying a handgun in the railway station in Inverness on Tuesday as he walked through the main concourse.
Police Scotland said the officer had breached new force policy.
A spokesman said he had been reminded of the strict criteria about the issue.
It was a sight more common in 2013 when a policy was introduced allowing firearms officers to carry handguns with them at all times while on duty.
However, after concerns from politicians, the chief constable of Police Scotland, Sir Stephen House, stated last October that specialist armed police officers in Scotland would only be deployed to firearms incidents or where there was a threat to life.

Ryan Thomas McManus, 31, from Ava Street in Belfast and Ryan Milligan, 29, from Manse Road in Dundrum were given seven-year terms for over 40 drugs offences.
They will serve half their terms in prison and half on licence.
A third man on charges died on Tuesday.
Connor Devenney, 36, from Dunwellan Park in Newcastle, County Down, appeared in court last week, when the Crown set out its case against the three men.
However, a judge was told that Devenney, who faced two charges linked to the operation, died on Tuesday night.
Passing sentence on McManus and Milligan, the judge said the pair were involved in a "widespread supply of a quantity of illicit drugs" that they distributed "both in the UK and elsewhere".
He said that on one level there was a degree of sophistication, due to the use of the internet and Bitcoin currency, but on another there was a lack of sophistication as they left a "forensic trail".
He said this trail allowed both the police and other authorities to "become aware of the criminal activity" that ultimately led to their arrest.
Last week, the court heard that Milligan and McManus were arrested on 5 August, 2013, when several properties they were linked to were searched and drugs were seized.
A crown prosecutor said that during the period of offending - which spanned from January 2012 to August 2013 - the pair received consignments of drugs that were delivered to addresses either occupied or controlled by them.
They also used a virtual mailbox facility in the centre of Belfast.
The court heard some of the drugs were purchased online using Bitcoin currency. Drugs seized included more than 4,000 Class A tablets, and over 2,700 doses of DPP, as well as cocaine and over 100 grams of herbals.
The Scottish Professional Football League is warning clubs to be on their guard against online fraud.
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Homes, businesses and a school are being evacuated in a village after a World War Two bomb was found in a quarry.
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A man's body has been found after a fire at a house in Darlington.
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A police officer in Inverness has been photographed carrying a firearm despite assurances that sidearms would only be deployed under special circumstances.
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Two men involved in an international drugs operation that included buying illegal substances on the 'dark web' using Bitcoin currency have been jailed.