He attributed the reasons for the low ranking to two leftwing youth rebellions in the past 40 years which turned universities into hotbeds of insurgency, and long neglect of facilities and academics.
Sri Lankan universities, due to limited intake capacity, by default only open their doors to 20,800 students or the top five percent that sit for the Advance Level exams.
The rest join the work force, pursue their high-education in foreign universities or their satellite branches in Sri Lanka.
A high number also enroll into professional qualifications in accounting, finance, management and marketing.
These are mainly professional British qualifications like Chartered Institute of Management Accounting, Chartered Institute of Marketing and Association of Chartered Certified Accountants.
Sri Lanka has one of the largest pool of people with these qualifications outside the UK.Academics said the universities have to pay to get the rankings done by various independent organizations.
The best known ones are by the London Times and The Guardian which publish international ranking tables annually.
None of the Sri Lankan academic institutions are listed in the 2009 list by the Times of the top 200 Asian universities.
Most foreign universities work closely with industry and receive large grants to carryout research work mostly in the science fields.
"Sri Lankan universities are little bit behind on research work and the academic publications. This also has an effect on the university rankings," Kshanika Hirumburegama, vice chancellor at Colombo University, whose Medical College is the second oldest science faculty in Asia after Calcutta.
India has seven universities in the Asian list thanks to the creation of Indian Institutes of Technology (IIT) universities, in major cities like Delhi, Bombay and Madras.
IIT is a heavily research-based university and works closely with hi-tech companies like Microsoft and Cisco. This helped to propel India as the regional IT hub.
"We want to increase our rankings," Samaranayake said.
"We are trying to improve our relations with industry to improve our research capacity. But there's some catching up to do, so we want to fast track the process."
Efforts by successive governments to allow private universities have been stalled because of opposition by political parties, mainly the Marxist Janatha Vimulthi Peramuna.
This has forced students who can afford it to go abroad for higher studies.
Higher education minister Vishwa Waranapala told a media conference that Sri Lankan parents pay over 60 million US dollars to educate their children overseas. Central Bank officials said the actual figure can be much higher.
"Every year 8,000 to 10,000 student leave Sri Lankan shores seeking foreign education, in the UK, US, Australia and Canada," Samaranayake said.
"A few get scholarships but most pay for it (foreign education) themselves."
Universities are rapidly increasing student enrollment which is currently at 20,800 students, up 6,000 from last year, Samaranayake said.
He said university enrollments are expected to go up even further with the ethnic conflict coming to an end and spending had also increased.
In 2004/2005 95,000 rupees were spent on a student every year. In 2008 the expenditure had gone up to 280,000 rupees.
Sarath Amunugama, vice chancellor of the Kelaniya University said there were growing calls for changes to academic syllabi to be more in tune with the times and to produce employable graduates.
"The university academia is planning to hold meetings to address the issues in higher education in Sri Lanka. The government has said it will provide the necessary budgets and counterparty funds."
Sri Lankan universities are 100 percent financed by the government.
Foreign universities rank themselves to attract overseas students that have to pay more than local students, Amunugama said.
He said French universities are not ranked, because they are also financed by the state.
"But you have to remember that one has to pay to get these rankings done," Samaranayake said.
“There's a cost we have to bear to conduct these ranking surveys."