The £5.3 million contract will be undertaken at the British Underwater and Test Evaluation Centre (BUTEC), which the company operates on behalf of the MoD.
The autonomous underwater targets, which are the size of torpedoes and simulate the radiated noise and target echo strength of a submarine, are used for training submarine crews to detect and classify targets.
They are also used for firing training torpedoes as part of ongoing weapon and platform acceptance trials for the Royal Navy's submarine fleet, including the latest Astute class.
Sarah Kenny, managing director of QinetiQ Maritime, said: "We are very pleased to have won this significant contract, further strengthening our extensive and deep working relationship with the MOD and the Royal Navy.
"The securing of this contract is a testament to the value for money and quality of the services already being delivered by QinetiQ in support of the Royal Navy."
QinetiQ which listed on the London Stock Exchange in 2006 after spinning out of the MoD, declined to comment on whether any provision had been built into the deal should there be a Yes vote in September's referendum on Scottish independence.
A spokesman said: "That wouldn't be for us to talk about. That would be for the M0D - it's their contract and their work."
But a MoD spokeswoman said that, with the UK government confident "the people of Scotland will vote for unity" in the referendum, "no contingency plans have been made" for the contract in the event of a Yes vote.
QinetiQ's platform readiness services team, based at BUTEC, will deliver the contract. Its work is underpinned by an extensive range of facilities and equipment to support the introduction of new, refitted and upgraded ships, submarines and helicopters into service to strict deadlines.
QinetiQ's platform readiness services have been delivered to a number of countries and navies beyond the MoD and the Royal Navy, including the US, Norway, Canada and Sweden, as well as constructors such as BAE Systems, Babcock and Thales.
Meanwhile, QinetiQ has also secured a contract with the European Space Agency (ESA) to develop a unique soft docking system for use at the International Space Station (ISS).
QinetiQ is currently developing and building and engineering model intended to be tested on the ground under a contract due to run until 2015. This contract is expected to lead to a further development phase lasting until 2017.
The International Berthing Docking Mechanism (IBDM) is said to allow two spacecraft to berth and dock with each other while ensuring an airtight connection.
Shares in Farnborough-based QinetiQ closed 2.3p or 1.08 per cent at 209.7p.