The punishment for fornication is stoning to death. But before this we need proof ie witnesses. Sometimes, it so happens that we know two people have been sleeping together but no one has actually seen them in this act. To my knowledge, the Islamic law requires that four witnesses must observe the two people doing this sin. So, in this age, should we disregard these witnesses (also there may be a case when there are no witnesses), and go for other measures for instance some medical tests that will prove that the two have had a sexual encounter?

First of all it must be understood that the punishment of fornication (zinā), according to the Qur’ān, is flogging the criminal with a hundred stripes, humiliating him and prohibiting his marriage with chaste women:

The man and the woman guilty of fornication, flog each of them with a hundred stripes and let not compassion move you in their case in the enforcement of the law of God, if you truly believe in Allah and the Last Day. And let a party of the believers witness their punishment. This man guilty of fornication may only marry a woman similarly guilty or an idolatoress and this woman guilty of fornication may only marry such a man or an idolator. The believers are forbidden such marriages. (24:2-3)

There are some forms of fornication in which a person compounds this crime by taking the law in his hands and spreading disorder and nuisance (rape is one example). In such cases, he can be administered severer punishments as mentioned in the Qur’ān; he can even be put to death in an exemplary way (stoning to death is one form of such an exemplary punishment). The Qur’ān says:

The punishments of those who wage war against Allah and His Prophet and strive to spread disorder in the land are to execute them in an exemplary way or to crucify them or to amputate their hands and feet from alternate sides or to banish them from the land. Such is their disgrace in this world, and in the Hereafter theirs will be an awful doom save those who repent before you  overpower them; you should know that Allah is Oft-Forgiving, Ever Merciful. (5:33-34)

The Qur’ān has in no way bound us to adopt a particular method to prove a crime; a crime stands proven in Islamic law just as it stands proven in accordance with the universally accepted legal methods endorsed by sense and reason. Consequently, if circumstantial evidence, medical check ups, post mortem reports, finger prints, testimony of witnesses, confession of criminals, oaths or any other method is applied to ascertain a crime, it is perfectly acceptable to the Islamic law.

However, there are two exceptions to this general principle:

i) If a person accuses a chaste and righteous man or woman having a sound moral reputation of fornication, then the Qur’ān insists that the accuser shall have to produce four eye witnesses:

Those who accuse honourable women and bring not four witnesses as an evidence [for their accusation], inflict eighty stripes upon them, and never accept their testimony in future. They indeed are transgressors. But those who repent and mend their ways, Allah is Oft-Forgiving and Most-Merciful. (24:4)

Circumstantial evidence or medical reports in this case are of no importance. If a person is of a lewd character, such things are of importance, but if he has a morally sound reputation, Islam wants that even if he has faltered, his crime should be concealed and he should not be disgraced in the society.

ii) To purge an Islamic state of prostitutes, who in spite of being Muslims, do not give up their life of sin, the only thing required, according to the Qur’ān, is that four witnesses should be called forth who are in a position to testify that they are prostitutes:

And upon those of your women who habitually commit fornication, call in four people among yourselves to testify over them; if they testify [to their ill-ways], confine them to their homes till death overtakes them or God finds another way for them. And the man and woman among you who commit fornication, punish them. If they repent and mend their ways, leave them alone. For God is Oft-Forgiving and most Merciful. (4:15-16)

Another point to be noted is that the Almighty does not like that a criminal confess his crime himself or that those who are aware of his crime report this matter to the authorities. This is evident from the wording of the law of wrongly accusing someone of fornication stated in the Qur'ān in 24:4 (See above).

The Prophet (sws)also is said to have said:

He among you who gets involved in such filth should hide behind the veil stretched out for him by Allah, but if he unfolds the veil, we shall implement the law of Allah upon him. (Mu'attā, Kitābu’l Hudūd)

Similarly, he once told a person:

If you had hidden the crime of this [person], it would have been better for you. (Mu'attā, Kitābu’l Hudūd)