Where did Ellen White say that God has left the church?

Using some of the words you gave me, I did a search for such a statement. I did not find it. Actually, I have a hard time thinking that Mrs. White made a statement such as you have asked for. I recall other statements she made, with which this one would be quite out of harmony.

Here’s a prime one:

During ages of spiritual darkness the church of God has been as a city set on a hill. From age to age, through successive generations, the pure doctrines of heaven have been unfolding within its borders. Enfeebled and defective as it may appear, the church is the one object upon which God bestows in a special sense His supreme regard. It is the theater of His grace, in which He delights to reveal His power to transform hearts (The Acts of the Apostles, 12).

If Mrs. White believed that God had left the church long ago, why would she stay with it?

It is possible that you may be thinking of a much more limited kind of statement, from the years between 1888 and 1901—the ones featured in A. V. Olson’s book Thirteen Crisis Years: 1888–1901. Here are some statements along this line, as collected in the book Last Day Events, pages 50, 51:

The voice from Battle Creek [the General Conference], which has been regarded as authority in counseling how the work should be done, is no longer the voice of God.—17MR 185 (1896). . . .

That these men should stand in a sacred place, to be as the voice of God to the people, as we once believed the General Conference to be—that is past.—GCB April 3, 1901, p. 25.

You will find, however, that Mrs. White did not continue to hold such a negative view. After the reorganization of 1901 addressed the serious problems, she took quite a different view. Here are several statements that she made after that reorganization (all found in Last Day Events, 55, 56). The last quotation is her final message to the Seventh-day Adventist Church in General Conference session, read to the assembly by the General Conference president, A. G. Daniells, on May 27, 1913:

We cannot now step off the foundation that God has established. We cannot now enter into any new organization, for this would mean apostasy from the truth.—2SM 390 (1905).

I am instructed to say to Seventh-day Adventists the world over, God has called us as a people to be a peculiar treasure unto Himself. He has appointed that His church on earth shall stand perfectly united in the Spirit and counsel of the Lord of hosts to the end of time.—2SM 397 (1908).

At times, when a small group of men entrusted with the general management of the work have, in the name of the General Conference, sought to carry out unwise plans to restrict God’s work, I have said that I could no longer regard the voice of the General Conference, represented by these few men, as the voice of God. But this is not saying that the decisions of a General Conference composed of an assembly of duly appointed, representative men from all parts of the field should not be respected.

God has ordained that the representatives of His church from all parts of the earth, when assembled in a General Conference, shall have authority. The error that some are in danger of committing is in giving to the mind and judgment of one man, or of a small group of men, the full measure of authority and influence that God has invested in His church in the judgment and voice of the General Conference assembled to plan for the prosperity and advancement of His work.—9T 260, 261 (1909).

God has invested His church with special authority and power which no one can be justified in disregarding and despising, for he who does this despises the voice of God.—AA 164 (1911).

I am encouraged and blessed as I realize that the God of Israel is still guiding His people and that He will continue to be with them, even to the end.—2SM 406 (1913).

If you will read the entire chapter of Last Day Events, you will see the whole sweep of the issue and get a good overview of the reasons why Mrs. White said what she did and why she was later able to say something quite different.

See also the preceding and the following questions and answers.