Limitation of skills: As mentioned earlier, the success and quality of the test will directly depend on the skills and experience of the penetration testing team. Penetration tests can be classified into three broad categories: network, system, and web application penetration testing. You would not get the right results if you make a person skilled on network penetration testing work on a project that involves testing a web application. With the huge number of technologies deployed today on the Internet, it is hard to find a person skillful in all three. A tester may have in-depth knowledge of Apache Web servers but might encounter an IIS server for the first time. Past experience also play a significant role in the success of the test; mapping a low risk vulnerability to a system that has a high level of threat is a skill that is only acquired with experience.

Limitation of time: Often, penetration testing is a short-term project that has to be completed in a predefined time period. The testing team is required to produce results and identity vulnerabilities within that period. Attackers on the other hand, have much more time to work on their attacks and can plan them carefully over a longer period. Penetration testers also have to produce a report at the end of the test, describing the methodology, vulnerabilities identified, and an executive summary. Screenshots have to be taken at regular intervals, which are then added to the report. An attacker would not be writing any reports and can therefore dedicate more time to the actual attack.

Limitation of custom exploits: In some highly secure environments, normal pentesting frameworks and tools are of little use and it requires the team to think out of the box, such as creating a custom exploit and manually writing scripts to reach the target. Creating exploits is extremely time consuming and is also not part of the skillset of most penetration testers. Writing custom exploit code would affect the overall budget and time of the test.

Avoiding DoS attack: Hacking and penetration testing is an art of making a computer do things that it was not designed to do, so at times a test may lead to a DoS attack rather than gaining access to the system. Many testers do not run such tests in order to avoid inadvertently causing downtime of the system. Since systems are not tested for the DoS attacks, they are more prone to attacks by scripts kiddies who are out there waiting for such Internet-accessible systems to claim fame by taking them offline. Script kiddies are unskilled individual who exploit easy to find and well-known weaknesses in computer systems to gain fame without understanding the potential harmful consequences. Educating the client about the pros and cons of a DoS attack should be done which will help them to take the right decision.

Limitation of access: Networks are divided into different segments and the testing team would often have access and rights to test only those segments that have servers and are accessible from the internet to simulate a real world attack. However, such a test won't detect configuration issues and vulnerabilities on the internal network where the clients are located.

Limitations of tools used: At times, the penetration testing team is only allowed to use a client approved list of tools and exploitation frameworks. No tool is complete, be it the free version or the commercial ones. The testing team needs to have the knowledge of those tools and will have to find alternatives to the features missing from it.