It later demolished some of the best-known monuments in the UNESCO world heritage site.
However if reports of cooperation between the two groups are confirmed, Palmyra could not only prove damaging for the Assad regime but also for Russia which has also been implicated in the controversy.
Sky News said it has not authenticated the most recent documents but believe they are genuine, based on previous leaks which have proven to be true.
The broadcaster obtained the documents through contacts it has established with a Free Syrian Army group which was originally from Islamic State's headquarters in Raqqa for the past 18 months.
The group is now living across the border in Turkey and helping smuggle defectors across.
The letter
The latest leaked documents, along with accounts from IS defectors further show the terror group has been colluding with the Assad Government for years, it is claimed.
According to Sky, the latest letter is in addition to the 22,000 files it obtained in March this year, which detailed revealing inside information on missions and IS members.
The latest handwritten letter on Palmyra appears to show a deal between the two sides that was struck before the city was taken by IS forces. A translated extract states: "Withdraw all heavy artillery and anti-aircraft machine guns from in and around Palmyra to Raqqa province."
Raqqa remains the defacto capital of the terror group and among its most tightly-held prizes.
One defector also told the British broadcaster the deal to hand Palmyra back was part of a series of agreements and deals "going back years".
But it seems the Syrian Government isn't the only one embroiled in the leak.
The defector also revealed IS has been co-ordinating movements with the Russian air force and militants were evacuated before the Syrian army took control of the city.
What Islamic State get
While the Syrian Government gets kudos and looks like it's on top of the terror group, Islamic State would be after a much-bigger prize: resources and more security.
The letter shows that among the deals made was one which asked for a safe passage of a driver through IS checkpoints "until he reaches the border with the Syrian regime to exchange oil for fertiliser."
Other defectors revealed they remain openly loyal to the group's belief and desire to establish a caliphate and only left following a series of disagreements.
Sleeper cells
Alarmingly, the leaked documents also show intelligence agencies were unaware of sleeper cells and foreign fighters being trained months before they were detected.
According to Sky, that revelation fuels fears particularly in the US that a network of undetected sleeper cells exist across Europe.
It is feared such cells would be capable of carrying out further terror attacks similar to that which took place in Paris and Brussels.
Among some of the documents is an order issued from IS headquarters codenamed "break the siege" which involved sending fighters over the border to "infidel countries" with a follow up paper a month later revealing it had reached "specialised areas."
A defector said Europe was the target and it was directed by Abu Mohammed al-Adnani (al-Shami), who has been linked to several fighters in northern Europe and who has a $5m bounty on his head.
Al-Adnani, whose real name is Taha Subhi Falaha, is regarded as the terror group's official spokesman.
According to Reuters, he grew up with a "love of mosques" and was a prolific reader.
The previous leaks
The latest leak is sure to deal a blow to Islamic State which is still reeling after a similar event back in March where the names and details of thousands of jihadis were released.
Those documents remain in the hands of British, US, German and Australian authorities after a disgruntled former IS fighter handed them over.
Abu Hamed left the group over "irreparable differences and a lack of vision" and took a memory stick of valuable information with him.
Among the cache was a recruitment form used by the group to sign up new members along with the details of the jihadists.
However, a French analyst investigating French fighters named in the documents said some were real while others were fake and would no doubt create several false leads.
