According to a Liberty Times article today, DPP legislators claim the cross straits shipping agreement paints the cross-strait shipments as domestic, not international, and that Taiwanese shippers are being denied permits by the Chinese authorities.
The government response is that as far as they know no Taiwanese shippers have applied yet, so nobody's been rejected and the allegations are empty; he asked the DPP to present evidence to the contrary.
Also see this post from Michael Turton.
Update in comments from Taiwan Echo:
More precise description of "no Taiwanese shippers have applied yet" is
"no Taiwanese shippers have submitted application to China yet"
which is not consistent with what I learned from the news -- that applications for entry were submitted to China but were denied.
Instead, Taiwanese ships were asked to get China's domestic permission.
Befre Chiang-Chen agreement effective on 12/15/08, Taiwanese ships didn't need to apply for China's domestic permission. Now they need to. That's how the agreement turns Taiwan into domestic part of China.