The download first became available about a fortnight ago, but subsequently some users began complaining of numerous problems.
These included faster than normal battery drain, some apps refusing to work and alarms failing to trigger.
The firm said it was now investigating the matter.
"We are committed to providing customers with the best possible mobile experience, and will ensure to resume the upgrading service at the earliest possibility," it added in a statement.
Several users posted messages on Samsung's UK Facebook page to complain that the firm had taken this long to act.
"Samsung keep telling us that they will let us know as soon as they find a fix, but in the meantime I am left with a phone that is next to useless," wrote one owner, Dylan Barlow, to the BBC.
The Galaxy S3 was first released in May 2012 running Android 4.0. Although it was later updated to 4.1, users were never offered the 4.2 upgrade - making the latest release the first for the handset since the start of the year.
The SamMobile news blog noted that one of the reasons for the firm to have released the upgrade at this point would have been to allow the phone to be compatible with its new Galaxy Gear smartwatch.
Another site, Android Police, has also revealed that the US network AT&T has pulled the 4.3 update for subscribers who own the newer S4 handsets, but has not yet released a statement.
This is not the first time such upgrades have caused issues,
In February, Vodafone UK and 3 Austria recommended iPhone 4S owners delayed an upgrade to Apple's iOS 6.1 operating system after complaints that some handsets were having problems making calls and connecting to the internet.
Days later the US firm released a new version of the software that fixed the problems.
Samsung has suspended a software update that upgraded UK-based Galaxy S3 owners to version 4.3 of the Android operating system - also known as Jelly Bean.