Conservative leader David Cameron said: "The Parliamentary Standards Commissioner must get to the bottom of what's happened in every case and we must look at the penalties that apply when rules like this are broken."
He said the self-regulating system was "at the heart of the problem" and that it might be necessary to change its structure.
Mr Cameron added that a system of imposing automatic fixed penalties on MPs who break rules might be appropriate.
The rules on overseas visits are there to ensure that no-one can accuse MPs of accepting foreign hospitality in return for political favours, for example pressing the UK government for financial assistance.
They require MPs to register such visits and then declare relevant trips in questions, motions or debates.
One of those who appears to have fallen foul of the code of conduct is Labour's Andrew Dismore, a member of the Commons Standards and Privileges Committee - the very body which polices MPs' behaviour.
He broke rules more than 90 times, following annual visits to Cyprus, by failing to declare the hospitality when raising issues about the island in Parliament.
In total, he has tabled more than 200 Commons questions about Cyprus since the last election in 2005, on topics such as missing persons from the island and its victims of past conflict between Turkey and Greece.
Politicians from all three main parties have breached rules
The Commons information office estimates it costs on average £149 to answer a written question.
Mr Dismore has also signed motions and led debates about Cyprus. However, he denies any wrongdoing and claims his questions about Cyprus were not sufficiently relevant to his trips to require a declaration.
Conservative David Amess has admitted failing to register a free trip to the Maldives - regarded as a "very serious" breach of the rules by the Committee on Standards and Privileges, according to the MPs' code of conduct.
He also accepts he did not register a second trip for almost a year, blaming an administrative error by his office staff.
During a debate he tabled about the Maldives in 2007, Mr Amess told the Commons how his "splendid visit" had given him "an early taste of paradise".
"No words can describe adequately just how beautiful the islands are," he added, before suggesting the UK Government "could be encouraged to do a little more than is being done at the moment" for the islands in the Indian Ocean.
Despite leading two debates about UK support for the Maldives and asking 15 questions about the islands, he failed to declare an interest. Referring to the MPs' code of conduct, Mr Amess told the BBC: "It is for the member to judge whether a financial interest is sufficiently relevant."
Liberal Democrat Norman Baker, who has been actively calling for a clean-up of Parliament following the expenses scandal, has admitted breaching the rules on 37 occasions.
MARK EASTON'S UK
What really struck me as I conducted the investigation is that the system of scrutiny surrounding the rules clearly does not work
In a statement to the BBC, Mr Baker accepts he failed to declare an interest when leading debates and tabling questions about topics such as human rights in Tibet. He has travelled to India twice, courtesy of the Tibet Society and the Tibet government-in-exile.
"I should have then declared a relevant interest in respect of the parliamentary activities you list," he said. "It is an unintended oversight that I did not."
The MP who heads the Commons Public Administration Select Committee, Tony Wright, told the BBC that such rule-breaking was "unacceptable" and that the system should be more transparent.
"Declarations should be the norm. It is quite proper for MPs to go on visits. Some of those visits will be financed by foreign governments. But... if they're lobbying on behalf of governments who have paid for their visits, then clearly we need to know about it."
The rules are enforced by MPs themselves. Breaches are only investigated if a formal complaint is made and there is no independent body to ensure that members stick to the regulations.
Shadow defence secretary Liam Fox has admitted breaking the rules on two occasions, having visited Sri Lanka five times in the past three years courtesy of its government. He failed to declare the hospitality when asking ministers how much UK aid had been given to Sri Lanka.
In a statement, Mr Fox said: "I should have noted an interest and will be writing to the registrar to make this clear." He blamed a "changeover of staffing responsibilities" for registering one of his visits more than two months late.
During the current Parliament, Gibraltar's government has funded 31 trips for MPs to attend an annual street party on the territory.
Labour's Lindsay Hoyle has been a guest at these National Day Celebrations three times. Following his visits he has asked 30 questions, tabled three early day motions and signed a further seven, all without declaring his interest.
Mr Hoyle also broke the rules by failing to declare an interest following registered trips to the Cayman Islands and the British Virgin Islands.
"I have never received or sought any financial benefit," he told the BBC.
Conservative Andrew Rosindell has been a guest of Gibraltar's government twice in recent years. He subsequently asked 48 questions and signed or sponsored nine motions related to the territory without declaring an interest.
Thirteen of his questions about Gibraltar were before a visit had been registered. The BBC put the matters to Mr Rosindell but has yet to receive a response.
The BBC has identified a further 10 MPs from all three major parties who have been guests of Gibraltar's government and shortly afterwards breached rules when signing motions or tabling questions about the territory.
The investigation has also identified three more Labour MPs and another Conservative who failed to declare an interest following visits to Cyprus.
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