The CJI said that while the standard and the quality of the service provided by Forensic Service Northern Ireland (FSNI) was high and there was a good turnaround in high profile cases, such as in terrorist cases, inspectors said performance was "relatively poor" when it came to lower priority "volume crime" investigations, such as burglaries.
Last year, High court judge, Mr Justice Weir criticised delays in providing reports for criminal proceedings.
He described the situation as "unacceptable" during a bail hearing in a drugs case.
The outburst forced the Justice Minister, David Ford, to defend the service and the financial constraints it had to operate under.
While the PSNI has its own in-house forensic branch that focuses primarily on crime scene work, it relies on the FSNI for the majority of its subsequent laboratory analysis.
Each year the service inspects 20,000 exhibits related to around 6,000 cases to produce over 9,000 reports.
The CJI found progress had been made in the speed reports were produced after a 2009 inspection identified similar concerns, but it said there was still "considerable work" needed.
The idea that the forensic laboratory barricades its door in the middle of the month because it has done all the work it's paid to do is absolutely unacceptable.
Mr Justice Weir
It said improvements would only come with "fundamental changes" to how forensic services in general in Northern Ireland were delivered.
Inspectors said funding arrangements should be looked at, with potentially the Department of Justice assuming the role of central funder rather than the FSNI being paid separately by a number of public organisations, such as the PSNI, Public Prosecution Service or Police Ombudsman's Office.
The CJI found there was a "mismatch" between the projected demands from customers for services and the actual availability and capacity of lab time in FSNI.
The Department of Justice is investing £15m in new laboratory space and cutting edge DNA analysis at the FSNI's headquarters in Carrickfergus.
Inspectors said this development could produce tangible improvements in outputs, but cautioned that was not inevitable.
The report stated: "It has the potential to deliver added benefits in terms of volume and timeliness of casework.
"But there is also a risk that this investment will not deliver the projected improvements due to inadequate planning, continued delays in the implementation of a new management information system and resistance to change among some staff."
CJI deputy chief inspector James Corrigan said there was a need for forensic services in Northern Ireland to be managed in a more joined-up way within the criminal justice system.
"This inspection found the quality of the scientific analysis and reporting being provided by FSNI was good," he said.
These positive developments along with the commitment of investment by the Department of Justice to fund new laboratory accommodation are however being undermined by backlogs and delays in the production of reports that are occurring as FSNI struggles to meet demand for its services.
James Corrigan, CJI
"The organisation has successfully retained external accreditation for its services from The UK Accreditation Service and criminal justice system customers of FSNI were also satisfied with the standard of advice and reports being provided.
"To deal with this issue, inspectors have recommended the development of a strategy to support the provision of a seamless service which addresses the funding and delivery of forensic services from crime scene to court.
"The strategy would require the input of the police and FSNI as the key providers of forensic services and should be directly linked to the requirements of prosecutors and the needs of the courts."
The deputy chief inspector said the police and FSNI should work together to better manage the demand for forensic science expertise and improve productivity within the laboratory.
"Inspectors welcome the steps that have been taken to date within FSNI to improve efficiency and the 20% increase in capacity already achieved in relation to some drugs analysis and exhibits submitted by the State Pathologist's Department," he added.
"This level of increased productivity needs to be urgently replicated within other specialisms operating within the organisation in order to reduce avoidable delay and minimise criticism that has recently been raised in court.
"We would also support FSNI's efforts to make better use of staff overtime by using it in a targeted manner to address backlogs and spikes in demand for forensic science and maximise value for money."
Responding to the report, Mr Ford said: "An action plan has been developed to address the issues identified by the inspectors and progress will be monitored closely.
"In particular, work is ongoing to develop a forensic services strategy that will support the delivery of good quality, timely, cost-effective and sustainable forensic services.
"The agency is also in the process of implementing several initiatives under its transformation programme.
"This includes a new case management system and laboratory information management system and new DNA technology which was launched in December.
"An essential part of the transformation programme is the capital investment I have made which will deliver a new laboratory at FSNI, which when complete will meet the highest of European standards.
"This investment will go some way in helping FSNI to respond to the ever changing demands of forensic science."