The image in that article seems to take as source Transparency International. If you access Malta page you'll see the link for the Corruption Perceptions Index for 2016. They don't have their own survey infrastructure. This means that the index is calculated as a composite analysis from surveys made by different organizations they consider to be reputable. For example the 2016 report has used the following sources pdf.
Let us analyze, for example, Freedom House and see which factors were considered major issues for Malta in 2016. They state:
In May 2015, a report from the UN special rapporteur on the human
rights of migrants found that migrants have difficulty integrating
into Malta’s economy and society. It noted the prevalence of labor
exploitation and weak enforcement of laws against such abuses. Also
that month, the Migrant Integration Policy Index ranked Malta 33 out
of 38 countries, underscoring problems in areas such as labor-market
mobility, education, and access to permanent residence.
and also refer to:
Separately during 2015, officials continued to investigate corruption
scandals involving the state-owned energy company Enemalta. In May,
the company’s former chief projects officer was acquitted of charges
that he had accepted bribes from an oil trader.
Another example of organization used in the same report is the World Economic Forum which for Malta it states the the item "1st Pillar: Institutions" has a downwards tendency (loosing quality). If you check closely (the item is drop down) you'll eventually reach sub items such as Irregular Payments and Bribes (Malta is in 49th position). You'll notice that WEF actually sees improvement in this point.
So although Malta does seem to be passing through a rough point at present, it is actually not consensual if the situation is improving or not. The situation in Malta is not unique in the EU. Many nations (including my own) have seen various scandals of political and financial nature. This includes José Socrates (former Prime Minister in Portugal), Silvio Berlusconi (former Prime Minister in Italy), and Joseph Muscat (although, as far as I know, this never got to court).
Conclusion: There are other examples but my conclusion is that, although the problem does exist, the graphic you linked might not be accurate regarding the actual progress Malta has been doing against corruption. If you read the article you'll notice that there is a cry for more to be done (against corruption). One can assume this particular pessimistic info-graphic might have been used to illustrate the problem. Nevertheless the international reaction (also stated in the article) is very real. There is a shock in seeing an activist murdered (its an extreme quite rare in the EU) and it will likely have a very significant cost for the country reputation.
UPDATE 1 - (2, December, 2017)
NOTE: emphasis in quotes are mine.
For people looking to be informed about the current status of corruption in Malta today's Guardian article, "MEPs looking into death of journalist 'disturbed' by trip to Malta", is an important one. It reports that:
MEPs on a fact-finding mission to Malta after the killing of the
investigative journalist Daphne Caruana Galizia have said they arrived
“seriously concerned” about the rule of law on the island and were
leaving “even more worried”.
Dispatched after the European parliament demanded that EU authorities
open a formal dialogue with Malta over the death, the delegation said
an apparent reluctance to investigate and prosecute major cases had
created a “perception of impunity”.
The MEP's mentioned in the Guardian are part of the PANA committee which deal with "Money Laundering, Tax avoidance and Tax evasion". The Guardian quoted Ana Gomes:
The Portuguese Socialist MEP Ana Gomes said the delegation found it
“extremely disturbing” that some of the officials it met did not
answer its questions. One, prime minister Joseph Muscat’s chief of
staff, Keith Schembri, read out a prepared statement, she said, while
another “never showed up”.
... and Sven Giegold:
The German Green MEP Sven Giegold said after two days of meetings with
government officials, regulators, local journalists media and civil
rights activists that he was particularly concerned about the island’s
police and attorney general.
Both had demonstrated “a high degree of unwillingness to investigate
and a failure to prosecute corruption and money-laundering”, Giegold
said, adding he left a meeting with senior police officials with an
impression of “incompetence”.
Giegold said publicly available information and even reports by the
anti-money laundering agency FIAU had failed to trigger
investigations, “protecting high government officials and financial
Glenn Bedingfield, a member of Malta Labour party (currently in power), has criticized the committee:
It is now obvious that the MEPs who talk of rule of law need to be
better versed in the spirit of the law. The law which state we are all
innocent till proven guilty. These MEPs came here with misconceptions
fuelled by Zammit Dimech, Roberta Metsola, David Casa, Jason Azzopardi
and Jonathan Ferris. They did not have an open mind. They think they
have the right to play judge and jury over Malta. This is very clear
in their statements today. Ana Gomez and her colleagues dont want to
be persuaded otherwise. Like those countries who are jealous of
Malta’s success as well as our observance of the real rule of law,
they are not satisfied.