According to the Scotsman, experts found cladding panels had not been fitted onto the building properly after two of the granite panels came loose in high winds in December 2011.
A further five were removed as a precaution.
In a report, however, it has now been revealed that following a detailed inspection of thousands of panels across the site, a range of defects have been found.
The problems have been blamed on poor workmanship during the construction process, but the company which carried out the work has since gone bust. As a result, the Scottish Parliament is unable to recover the costs of the damage.
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In its report, it said the panels removed in December 2011 had not been installed in accordance with the design and a full technical inspection was ordered of all 8,600 exterior cladding panels across the complex.
Remedial works were carried out but Watson Stonecraft Ltd, which installed the cladding panels, went into liquidation and was dissolved in 2012.
Independent Lothians MSP Margo MacDonald blamed the "rush to finish" the building for the problems.
She said: "I'm not surprised at this. There was a cast of thousands involved at the end. We said at the time there were bound to be things that showed up over the course of time.
"There was a lot of pressure to finish because the Queen was coming on a set date.
"If it's because there has been poor workmanship and perhaps the wrong materials, they could go at any time."
The Holyrood building opened in October 2004 and cost £414m to construct.
(JP/CD)
