I am trying to transform xml to rtf using fop-0.90alpha1. But I am getting transformation exception as follows:

This only happens if output format is rtf. It does not occur for PDF output.

The RTF renderer isn't nearly as complete as the PDF renderer.
In other words, you used a feature which isn't yet supported
for RTF output.

Line 12 (<fo:page-sequence master-reference="A4">) is the part of xslt that
 is pointed out in the exception to be cause of the exception.

The reference is bogus. The real problem has probably something to do
with a width or height or something else given in percents. You could
try to replace it by an absolute measurement (pt, or mm).