The APFA's executive officer, Helen Jenkins, has also accused the department of "failing in its duty of care" to protect the industry from the major biosecurity risk, white spot disease (WSD).
Recent department figures seen by the ABC show that 71 per cent of imported green prawns tested positive for the disease, which is not a risk to humans but is a major threat to the aquaculture industry.
"I was absolutely horrified; it's a very scary figure and means that most of the stuff coming in has white spot," Ms Jenkins said.
"It is not looking like the testing regime has been correct because if they were testing every container, as they say they do, then something is not right."
The department boosted its testing of imported prawns following the WSD outbreak on farms along the Logan River in south-east Queensland in December last year.
The recent figures show that of the 21 batches of prawns coming in at the time that a ban on imports was announced, six were cleared while 15 (71 per cent) tested positive for WSD.
The figure is considerably higher than what the department was initially detecting, prior to stepping up its testing methods for white spot.
From May to December last year, the department rejected 17 per cent of green prawn imports due to positive WSD tests.
That is based on government figures that showed, of the 448 consignments that arrived in Australia in that period, 73 were rejected due to WSD detections.
"I would say [the department] have dropped the ball and if they knew about it in August last year, that was well before our farms started stocking [for the current season]," Ms Jenkins said.
Source: ABC