A revised planning application has been submitted by National Museums Liverpool for the new Museum of Liverpool, already on site at the Pier Head.
The new application seeks permission to change the limestone cladding from Travertine to Jura limestone, as well as increased viewing platforms and better ramps for the disabled.
Danish architects 3XN were dismissed from the scheme last year and replaced by Manchester-based AEW over rows about costs and design control.
A spokesman for NML said: "The original material poposed for the cladding of the Museum of Liverpool, Travertine limestone, has been proven, after testing, to be unsuitable for the building.
"The open face of the stone has natural fissures which have become pitted with black algae and some of the panels have fractured.
"An alternative limestone, Jura, has been sourced and this is much finer grained with a closed surface which will not attract the same degree of growth and can be surface treated to ensure that it remains pristine and can be protected against graffiti.
"This is now subject to a new planning application. Jura has been used on many major public buildings, including the Royal Danish Opera House in Copenhagen, a building of quality."