Officials from the state's Department of Environmental Protection (DEP) have not only found the drugmaker guilty of violating numerous environmental regulations, but also allege its staff and attorneys "repeatedly delayed or impeded the investigation" during an inspection of a pilot research vaccine plant at West Point, where Merck has its biggest production site.
The investigation was triggered on June 13, when operators at the plant poured 25 gallons of potassium thiocyanate, used to scale up the production of one of Merck's experimental vaccines, down the drain.
The discharge entered the Upper Gwynedd wastewater treatment plant through its sewage collection system, interacted with chlorine and emerged in the Wissahickon Creek, where the released cyanide killed more than 1,000 fish.
The release prompted Philadelphia to shut down two major drinking water intakes which are supplied by the Wissahickon Creek in the East Falls section of the city.
What is more, health officials had to place recreational advisories on the Wissahickon Creek and Schuylkill River, which have all now been lifted.
Despite the environmental damage, the health warnings and the concerns in the local population, it took Merck a week to inform the US Environmental Protection Agency (EPA) that the release came from one of its plants, though the company insists it reported the incident the day it discovered it was caused by its facility.
The next day, June 21, DEP inspectors visited the site but according to the department were forced to spend too much time trying to gain access to certain areas and personnel, to the extent they felt hindered.
"We strongly disagree with the characterisation 'delayed or impeded' used by the DEP," Merck spokeswoman Connie Wickersham told In-PharmaTechnologist.com, refusing to go into details to rebut the department's findings.
"We have been cooperating closely with federal and state regulators and are expecting to hear what the sentence will be."
The DEP will not issue a fine until the investigation is completed and the same is the case with the EPA, which has said Merck could be hit with up to $32,500 (€25,000) per day per violation in civil penalties.
State regulators have sent a notice of violation to Merck requesting information about other chemicals that could have been involved in the Wissahickon fish kill and a description of the measures that the company will take in the future to prevent pollution.
"There is certainly some problem solving that needs to happen here," DEP spokesman Dennis Harney told In-PharmaTechnologist.com.
"We know it is human error that led to this environmental disaster, our focus is now on establishing what led to this error, be it inadequate training or something else."
An internal investigation by Merck on the incident is continuing and no disciplinary action has been taken as yet.
The drug giant has until August 18 to reply to the DEP's request for more information and Merck is considering its response carefully.
This appears wise in view of the suspicion the drug manufacturer has created among environmental groups and local residents; last week the routine release of a high-protein solution into the sewage system, which in the past has gone unnoticed, resulted in another investigation by the DEP, animated by the local community and the media.
The foam generated by the solution is harmless to both humans and wildlife in the creek and Merck has a permit for its discharge, still its high amount, which was due to Merck gearing up for the launch of four new vaccines - including Gardasil for cervical cancer - was enough to get the regulators involved.
To allay fears Merck has installed a defoaming agent which knocks the bubbles down and will be hoping the waters in the creek will not be murky from now on.