Israeli troops have seized many Hamas MPs and ministers
He was held when troops burst into the house early on Saturday, his wife said.
The Israeli military confirmed the detention of Mr Shaer, who is a senior member of the governing Hamas movement, which does not recognise Israel.
Israel has detained about 30 MPs and a third of the cabinet since the capture of an Israeli soldier in June.
Mr Shaer's wife added that he had been in hiding since Israel began its crackdown in late June.
He was rarely home during that period, she said.
An unnamed Israeli army spokesman quoted by AFP news agency said the detention was "part of our fight against the radical Hamas movement".
'Sorry, madame'
According to the detained man's wife, "several" military vehicles circled the house before dawn after which troops came to the door.
An officer told her after checking their identity documents: "Sorry madame, but your husband has to come with us".
"He let him first say goodbye to our four children," she told Reuters news agency.
Israel's crackdown has largely focused on the Gaza Strip, Hamas's stronghold, but politicians from the Islamist movement have also been detained in the West Bank.
Its position is that Hamas is a terrorist organisation and its leaders are therefore "targets for arrest".
In a separate development, an Israeli soldier was shot dead by a Palestinian gunman in the West Bank, the army said.
The gunman was then shot dead, officials say. The incident happened at a checkpoint near the city of Nablus.
West Bank territory
On Saturday, in a pre-dawn raid, Israeli soldiers seized Nasser al-Shaer at his home in Ramallah in the occupied West Bank. Al-Shaer is the Palestinian Deputy Prime Minister and a top official of the Hamas militant group.

The Israeli military confirmed the detention of al-Shaer. Israel has been cracking down on the Hamas movement, which does not recognise Israel, for the last seven weeks. Al-Shaer is the highest ranking Hamas member to be detained. 30 members of Palestinian National Authority parliament have also been detained during the crack-down.

Nasser al-Shaer, a former university professor, is known as a pragmatist in Hamas. Palestinian officials accused Israel of undermining their efforts to form a broad government coalition.

The West Bank was captured by Israel from Jordan in the 1967 Six-Day War and is considered by the United Nations and most countries to be under Israeli occupation. Some Israelis and various other groups prefer to refer to it as "disputed" rather than "occupied" territory.