The charges were dismissed after the ministry withdrew them in the Auckland District Court on Tuesday.
In a written judgment, Sharp criticised the process the ministry followed in gaining a warrant to search Platt's Greenhithe property. An out-of-date form, with no information on Platt's rights, was used.
The warrant was executed seven days after the Biosecurity Regulations and Search and Surveillance Act came in and the ministry had not updated records, Sharp said. "There is no excuse for a Government department getting it that wrong."
Platt denied a ministry claim he was given a letter during the raid explaining his rights. The ministry had no copy and Sharp believed "good witness" Platt. "This aspect of the warrant was sloppy."
Clones of Platt's computer hard drives were taken, including one with information about hospital patients where Platt's wife is assistant chaplain and the ministry "continues to fail to advise exactly what is on the clones", Sharp said.
Platt told the Herald on Sunday he will seek "substantial" compensation for damage to his reputation and "two-and-a-half years of distress, misery and costs".
Platt was charged two years after simultaneous dawn raids on his Greenhithe property, the Botanic Gardens and the properties of the gardens' curator, Jack Hobbs.
Only Platt, who represented himself in court, was charged.
Ministry compliance director Dean Baigent said the clones would be destroyed.
He acknowledged mistakes, but pointed out the judge had said the ministry did not act in bad faith. The warrants were the first after changes to the law and the mistakes had not been repeated. No staff had been disciplined.